The federal government is staring down a shutdown as a handful of ultra-conservative House Republicans remain opposed to a short-term agreement to keep the government funded. 

The current spending laws expire at 11:59 p.m. Sept. 30. Without a deal by that night, funding will lapse and many government functions, including some health care programs, will temporarily stop. 

Here’s how a shutdown will, and won’t, impact health agencies and services:

Medicare, Medicaid and Social Security won’t be impacted — at least initially

The Centers for Medicare and Medicaid Services (CMS) said it will have “sufficient funding” for Medicaid through the first three months of fiscal 2024 based on funding that has already been appropriated. 

Medicare and Social Security are mandatory entitlement programs funded by taxes and premiums, so they aren’t dependent on Congress. That means benefits will continue as normal. 

However, administrative actions like benefit verifications and issuing replacement Medicare cards will be paused for the duration of the shutdown.  

Open enrollment for the Affordable Care Act exchanges begins Nov. 1. According to the Health and Human Services Department (HHS) contingency plan, CMS “will continue Federal Exchange activities, such as eligibility verification,” using leftover fees from last year that were paid by insurers.

The Department of Health and Human Services will largely be shielded

This would mark the first time since 2013 that the federal health agency would be impacted by a government shutdown. That shutdown lasted just more than two weeks.

The 2018 shutdown, which came amid a dispute between House Democrats and then-President Trump over border security, lasted more than 30 days, but much of HHS was already funded because its annual appropriations bill had been signed into law. 

In a contingency planning document updated last week, HHS said its COVID-19 response will continue, as will clinical research. The Food and Drug Administration (FDA) will continue drug and medical device reviews, because those are funded by industry-paid user fees. 

HHS said it will “continue to protect human life and property,” such as monitoring for disease outbreaks, managing high-risk recalls and drug shortages. The agency is also responsible for caring for patients in the hospital onsite at the National Institutes of Health (NIH), though it will only be able to admit “medically necessary” patients.

The Centers for Disease Control and Prevention (CDC) will continue working on outbreak response, laboratory functions, the President’s Emergency Plan for AIDS Relief (PEPFAR) and emergency operations. 

The CDC would also continue the World Trade Center Health Program as well as the Vaccines for Children program, which are supported through mandatory funding.

But the shutdown would hit federal workers the hardest 

HHS said 42 percent of the agency’s employees — more than 37,000 people— would be furloughed without pay beginning on the second day of a funding lapse. 

The remaining 58 percent of staff are considered “excepted” and will have to work unpaid for the duration of the shutdown.

All federal employees will receive back pay after the shutdown ends, but federal contractors do not have that guarantee, including those who work maintenance or food services jobs.

Doctors and hospitals could continue to submit bills to Medicare and get paid, but the staff shortage could result in reimbursement delays. 

According to a 2014 Government Accountability Office report analyzing the 2013 shutdown, grants management activities at NIH effectively ceased because of employee furloughs, although most current grant recipients were able to draw down funds. 

NIH had to reschedule the review process for more than 13,700 grant applications because of the shutdown. 

Additionally, new patients were prevented from registering for clinical trials, before NIH recalled a small number of employees to reopen the registry. 

The staffing shortages could also impact Medicare application processing. 

According to the Committee for a Responsible Federal Budget, a nonpartisan fiscal policy think tank, more than 10,000 Medicare applicants were turned away each day during the 1995-1996 shutdown.