After administration officials wrote in court filings that nearly 1,000 fired Health and Human Services employees were not subject to a Wednesday block, a federal judge held an emergency meeting to specify her intent to the contrary.
The judge's initial temporary restraining order required federal agencies to temporarily halt reductions in force (RIFs) affecting workers represented by bargaining units that first filed on Sept. 30 to block any cuts attributed to the government shutdown. The administration, in filings, said that many of those to whom it had issued RIFs were unaffected by the order, as many departments and agencies had stopped recognizing those collective bargaining units over the summer in compliance with a March executive order.
On Friday, Judge Susan Illston held an emergency hearing in which she specified that multiple federal unions that were not among the case's plaintiffs would also be included under her temporary block. Further, at the plaintiffs' request, she specified that members of the collective bargaining units the agencies had stopped recognizing were similarly covered by the temporary restraining order.
An order signed later that evening set the clarifications in ink "because defendants expressed an inaccurate interpretation of the [temporary restraining order] provisions." It noted that the government's decision to stop recognizing the collective bargaining units are still under legal dispute.
Multiple federal departments including HHS were also required by midday Monday to provide updated numbers on the RIF notices they had sent. At HHS, the tally stands at 954 RIF notices "not inclusive of those that have since been rescinded." That's down from Friday's 982 RIFs, as Deputy Assistant Secretary for Human Resources and Chief Human Capital Officer Thomas Nagy Jr. wrote in Monday's declaration that he had "become aware that HHS has rescinded additional RIF notices."
A chart of the RIFs accompanying Monday's declaration showed 362 RIFs across various offices at the Centers for Disease Control and Prevention, including the agency's Office of Communication, Office of Public Health Ethics, the National Center for Chronic Disease Prevention and Health Promotion, the National Center for Health Statistics and others.
Judge blocks Trump administration's shutdown layoffs
UPDATED: Oct. 15 at 4:45 p.m.
A California judge has issued a temporary restraining order to halt layoffs at federal agencies under the ongoing government shutdown.
Two key unions for government workers—the American Federation of Government Employees and the American Federation of State, County and Municipal Employees—sued the Trump administration on Sept. 30 in anticipation of a shutdown as the White House indicated it would lay off workers through reductions in force. Those RIFs began earlier this week at federal agencies, including the Department of Health and Human Services (see below).
District Judge Susan Yvonne Illston said in the order that the administration took advantage of the shutdown to execute the job cuts. She ordered the feds not to act on RIFs it already conducted, to provide details on those RIFs and not to implement any further reductions under the restraining order.
AFGE National President Everett Kelley said in a statement on the ruling that "the administration’s move to fire thousands of federal employees who are already going without pay during the government shutdown is not only cruel but unlawful."
"These are dedicated public servants who keep our nation running—protecting public health, supporting education, ensuring fair housing and driving economic growth," Kelley said. "We are pleased with the court’s ruling halting these unlawful terminations and preventing the administration from further targeting hardworking civil servants during the shutdown.”
The parties will meet for a hearing on a preliminary injunction down the line, per court documents.
Reductions in force begin at HHS, with some hiccups at CDC
UPDATED: Oct. 13 at 1:25 p.m.
The Trump administration has begun to make good on its threat to fire federal workers during the government shutdown, with cuts confirmed to affect the Department of Health and Human Services (HHS)—including roughly 600 at the Centers for Disease Control and Prevention (CDC) after taking into account hundreds of missent termination notices and rescindments.
The reductions in force (RIFs) were confirmed Friday by Office of Management and Budget Director Russ Vought in a four-word social media post: "The RIFs have begun." Vought's office had been threatening the layoffs as a potential consequence of a prolonged shutdown, and Vought himself has long been a vocal proponent of shrinking the federal workforce.
A spokesperson for HHS confirmed that its employees are included in the reductions, though did not specify how many workers or which agencies are being affected.
"HHS employees across multiple divisions have received reduction-in-force notices as a direct consequence of the Democrat-led government shutdown," the spokesperson said in an emailed statement.
"HHS under the Biden administration became a bloated bureaucracy, growing its budget by 38% and its workforce by 17%. All HHS employees receiving reduction-in-force notices were designated non-essential by their respective divisions. HHS continues to close wasteful and duplicative entities, including those that are at odds with the Trump administration's Make America Healthy Again agenda."
The RIFs themselves do no appear to have been conducted as intended. Reporting from multiple outlets over the weekend described hundreds of CDC employees who had receiving notices of their termination in error, with rescindments going out on Saturday.
According to the American Federation of Government Employees (AFGE), more than 1,300 CDC workers had received RIF notices on Friday, and about 700 received another email rescinding that termination within 24 hours.
Officials speaking with press said the mistake stemmed from a coding error, and highlighted teams at the Morbidity and Mortality Weekly Report publication, those addressing the measles outbreak and the Epidemic Intelligence Service among those who were called back. On the other hand, the CDC's entire Washington office appears to have been released.
Yolanda Jacobs, president of AFGE Local 2883, said Monday "the accounts of irreparable harm being done continue to unfold: Human resource workers brought back from furlough and forced to send themselves RIF notices with effective dates of December 8, 2025; CDC mental health professionals who have supported employees affected by the August 8, 2025, shooting attack on CDC’s Atlanta-based headquarters, now finding themselves facing termination. The administration has more than delivered on its promise to traumatize federal employees."
HHS' contingency plan for the shutdown saw 32,460 employees furloughed. Mandatory health payment programs like Medicare and Medicaid as well as OIG's Health Care Fraud and Abuse-related activities have not been interrupted due to the shutdown.
That said, the partial-staffed department was already running with thousands fewer employees due to reduction efforts from the Trump administration and the Department of Government Efficiency earlier this year. Nearly 2,000 had been terminated from the CDC prior to the roughly 600 affected this week.
The plans to release employees during a shutdown has already been challenged on legal grounds by government unions. Everett Kelley, national president of AFGE, on Friday called the reductions "disgraceful" alongside broader calls for Congress "to do their jobs" and cut a deal to end the shutdown.
"In AFGE's 93 years of existence under several presidential administrations—including during Trump’s first term—no president has ever decided to fire thousands of furloughed workers during a government shutdown," Kelley said in a statement. “AFGE is currently challenging President Trump’s illegal, unprecedented, abuse of power and we will not stop fighting until every reduction-in-force notice is rescinded.”
In a joint statement Monday, the heads of four infections disease associations (the Infectious Diseases Society of America, the HIV Medicine Association, the Pediatric Infectious Diseases Society and the Society for Healthcare Epidemiology of America) said the CDC's RIF confusion was "completely reckless" and said cuts to the agency's core functions and scientific leadership "will cripple the agency that keeps our country safe."
“Even prior to the latest round of layoffs, clinicians across the country reported dangerous interruptions in access to services including laboratory testing, public reporting and expert analyses of outbreak data and publication of clinical guidelines, all of which directly impact patient care. Additional layoffs will further erode CDC’s ability to perform essential duties and put our country’s health at risk," they said, calling for a reversal of the firings and for a spending accord in Congress.
Earlier this week the administration floated a belief that it is not required to provide backpay to all furloughed federal workers. The initial days of the shutdown also saw President Donald Trump suggest the funding lapse would give him "unprecedented opportunity" to trim down "Democrat Agencies."
Meanwhile, the administration took steps to block billions in appropriated federal funds, with the president saying during a Thursday cabinet meeting his administration planned to permanently cut "very popular Democrat programs that aren't popular with Republicans."
UPDATED: Oct. 7 at 10 :30 a.m.
Independent Dispute Resolution process continuing amid shutdown
The Centers for Medicare and Medicaid Services has confirmed the process for providers and payers to settle out-of-network care charges is up and running—for now.
In a notice published online late last week, the agency said the Independent Dispute Resolution (IDR) process "will remain in operation," meaning that parties may keep submitting their disputes via the online portal and that licensed mediators will continue to process those disputes under the established dispute timelines.
"However, please note that a prolonged lapse in appropriation may cause delays in the review and processing of IDR complaints and response times to inquiries," CMS wrote online.
The IDR process has taken flak since opening in 2022 for its extensive backlog of disputes, which officials said was fueled by unexpectedly high volumes of filings.
CMS recently issued a report stating that federal departments' recent steps to address IDR backlog had "delivered remarkable improvements" and that as of Sept. 19 "IDR entities are now resolving disputes faster than they are submitted." Those efforts, per the report, include implementation of automated validations, education events for stakeholders to improve the quality dispute filings, the publication of additional guidance and more hands-on work with licensed IDR entities.
As for the shutdown, media reports as of Oct. 7 suggest no meaningful debates are being held between Republicans and Democrats to reopen the government or address key negotiation issues like extending enhanced premium tax credits for Affordable Care Act plans.
UPDATED: Oct. 3 at 10:00 a.m.
Extending the enhanced ACA tax credits is broadly popular, poll finds
Enhanced premium tax credits for Affordable Care Act plans is at the center of the ongoing government shutdown, and a new poll finds that extending these subsidies is largely a popular move.
KFF's latest Health Tracking Poll surveyed 1,334 adults between Sept. 23 and Sept. 29, finding that 78% overall believe the tax credits should be extended beyond their expiry at the end of this year. When breaking the results down by political affiliation, a majority in all groups supports an extension.
Almost all (92%) of Democratic voters said they support extending the credits, as did 82% of independents. Fifty-nine percent of Republicans surveyed also said that the enhanced subsidies should be extended.
The survey further broke the Republican respondents down to Make America Great Again supporters and non-MAGA supporters, and found a majority in both groups support an extension. Extending the tax credits was backed by 57% of MAGA voters and 70% of non-MAGA Republicans, per the survey.
Among individuals who said they buy their own coverage, largely through the insurance marketplaces, 58% said they heard either "a little" or "nothing at all" about the expiration of the tax credits.
“There is a hot debate in Washington about the looming ACA premium hikes, but our poll shows that most people in the marketplaces don’t know about them yet and are in for a shock when they learn about them in November,” said KFF President and CEO Drew Altman.
Close to half (42%) said they would go without coverage if their insurance premiums doubled next year, as KFF estimated in a recent study.
Should the tax credits ultimately expire, 39% said they would blame President Donald Trump for this while 37% said they would blame Republicans in Congress. Twenty-two percent said Democrats in Congress hold the largest share of blame.
Published Oct. 1 at 12 noon ET
CMS issues guidance calling quits on expanded telehealth flexibilities
On day one of the government shutdown, the Centers for Medicare & Medicaid Services (CMS) sent out a Medicare Learning Network Connects Newsletter offering guidance on Medicare billing and telehealth services during the lapse in appropriations.
The CMS reaffirmed in the guidance that pandemic-era expanded telehealth flexibilities have ended for Medicare beneficiaries. Per standard course of action, the CMS has directed Medicare Administrative Contractors (MACs) to implement a temporary claims hold for 10 business days on telehealth claims.
Assuming the hold starts Oct. 1, claims will begin to be processed Oct. 15. The guidance says that providers can still submit claims during the temporary hold, but they will not receive payment.
The claims hold is meant to avoid the reprocessing of claims in the event that Congress re-ups the flexibilities.
According to pre-pandemic rules, Medicare beneficiaries must be located in a rural health clinic or rural hospital to conduct a telehealth visit with a provider in another geographic location, excluding mental health services. Audio-only visits are no longer allowable.
Some other telehealth services from before the pandemic are still allowed, such as telehealth visits for home dialysis related to end-stage renal disease. The CMS also notes that some types of practitioners can no longer render telehealth services. Such providers include occupational therapists, physical therapists, speech-language pathologists and audiologists.
Certain accountable care organizations under the Medicare Shared Savings Program can still perform telehealth services regardless of the beneficiary’s geographic location and beneficiaries can conduct visits in their homes.
The CMS says providers who continue performing telehealth services should consider sending an Advance Beneficiary Notice of Noncoverage, a notice typically required to be sent to patients when Medicare won’t cover their services. It also said providers should consider holding telehealth claims.
“In the absence of Congressional action, practitioners who choose to perform telehealth services that are not payable by Medicare on or after October 1, 2025, may want to evaluate providing beneficiaries with an Advance Beneficiary Notice of Noncoverage,” the CMS wrote. “Practitioners should monitor Congressional action and may choose to hold claims associated with telehealth services that are not payable by Medicare in the absence of Congressional action.”
The Alliance for Connected Care issued a statement commending the CMS for the claims hold.
“We appreciate rapid CMS action this morning to direct all Medicare Administrative Contractors (MACs) to implement a temporary claims hold,” Chris Adamec, executive director of the Alliance for Connected Care, wrote in an email. “While this does not mitigate the patient access challenges of the telehealth lapse, it may help to reduce [the] administrative burden associated with it.”
“Most providers and hospital systems are taking calculated risks to continue care during this time, but long-term continuity depends on action by our telehealth champions in Washington to restore these flexibilities and ensure retroactive reimbursement,” Kyle Zebley, executive director, ATA Action and senior vice president, public policy at the American Telemedicine Association, said in a statement. “Medicare patients woke up this morning without telehealth coverage for the first time since the pandemic, five years ago. Our healthcare services are regressing, falling woefully short for millions of patients in need.”
What will and won’t continue at HHS
The Department of Health and Human Services (HHS) will furlough 32,460 employees, or 41%, according to the agency’s staffing contingency plan released Monday. The estimate is called a “second-day staffing level,” based on the number of employees the department expects to need on the second day of a shutdown after staff have completed necessary shutdown functions.
The actual number of employees remaining at the agency will fluctuate throughout the shutdown, depending on the activities that need to occur.
This plan reflects the anticipated number of staff who will be on board during the second business day after a funding lapse, following the completion of initial shutdown activities. HHS expects to complete initial shutdown activities within the first day after receiving notification from OMB to implement the contingency plans. The plan has been updated to reflect staffing and funding levels as of July 2025.
Medicare, Medicaid, OIG's Health Care Fraud and Abuse-related activities, and other mandatory health program payments will continue.
HHS will continue to perform certain functions, including direct medical services through the National Institutes of Health and Indian Health Services, emergency preparedness for disease outbreaks and natural disasters, and medical device and drug reviews.
“Some HHS agencies have mandatory, multiple-year, carryover, or user fee funds which are not affected by a lapse in annual appropriations,” the contingency plan says. “A total of 35,096 staff are estimated to continue to be paid by these funds and remain working during a lapse in appropriations.”
CDC communications to the public will be interrupted.
Global strategy firm Capstone projects a short-term government shutdown will have "minimal impact" on operations at HHS. According to HHS' contingency staffing plan, the agency expects staff supporting mandatory funded activities like Medicare, Medicaid and other mandatory health program payments from furloughs, Capstone noted in a report released Wednesday morning.
CMS will maintain the staff necessary to ensure that payments for mandatory federal healthcare programs, such as Medicare and Medicaid, continue. Potential staff losses via furloughs and terminations may lead to minor administrative delays, Capstone wrote.
NIH research grinds to a halt
As the U.S. government shuts down due to a failure of Congress to pass a spending bill, the National Institutes of Health is implementing a contingency staffing plan that will again roil a research apparatus that has already been heavily disrupted during the second Trump administration, Fierce Biotech reports.
At FDA, new applicants put on hold
With a government shutdown now in effect, the U.S. FDA—already shaken up by headcount reductions earlier this year—has sought to keep many of its functions running for the foreseeable future, Fierce Pharma reports.
But the shutdown, which at least one former senator predicts could drag on for a month or more, will still have very real consequences for biopharma companies that don’t yet have an application in with the regulator, experts warned.
The FDA has committed to retaining 86% of its staff—equivalent to 13,872 workers—during the shutdown, according to a contingency plan posted on the Department of Health and Human Services website.
In its contingency plan, HHS noted that the FDA will not be able to accept applications for new drugs, generics, biologics, biosimilars or medical devices that require payment of a user fee while the shutdown is in effect. If companies have not already filed for a review of their products, they will now have to wait until Congress reaches a funding accord.
Healthcare stakeholder statements
“Nurses are very clear that Republicans are to blame for any government shutdown; they manufactured this impasse by refusing to negotiate with Democrats as a means to further degrade and gut critical public services and to advance an agenda to privatize vital functions currently provided by the federal government for the greater public good,” National Nurses United wrote in a statement to the press.
“We urge Congress to come together to fund the government for Fiscal Year 2026 and extend vital health and safety net programs that millions rely on,” the Catholic Health Association said. “A government shutdown jeopardizes the health and stability of millions of families—especially those living paycheck to paycheck and communities that depend on essential services. The ripple effects of inaction extend across the economy, deepening hardship for those already most vulnerable.”
“A shutdown only stifles access to care, impacts training opportunities for preparing the next generation of physicians and leaves our patients scrambling for alternative care—or worse yet, going without care,” the American Academy of Family Physicians wrote in a statement. “On behalf of family physicians across the U.S., we urge our elected leaders to recognize the human faces behind every policy decision and reach a swift bipartisan resolution that preserves access to care.”