A partial government shutdown that took effect Jan. 31 has entered its fourth day after Congress failed to meet a Jan. 30 deadline to pass a revised funding package.
Although the Senate voted 71-29 late Jan. 30 to pass the revised package, the measure still must clear the House and reach President Donald Trump’s desk. The funding lapse affects large portions of the federal government.
The package includes appropriations bills to fund five agencies, including HHS, through Sept. 30. It also includes a two-week stopgap measure to fund the Department of Homeland Security, which has been a key sticking point holding up negotiations.
The House is scheduled to take a procedural vote Feb. 3 at 11:15 a.m. Eastern time, with a final passage vote expected around 1 p.m. Eastern time, The New York Times reported Feb. 3.
Three things to know:
1. HHS updates lapse plan summary. HHS’ fiscal 2026 lapse plan summary shows 23,128 employees, or 31% of staff, would be furloughed, with 51,082 employees retained. This is significantly better than prior projections, partly because FDA and Indian Health Service have full-year appropriations and will not experience a lapse, the plan said.
- CMS: All 5,733 employees are retained through non-discretionary funding. Services including Medicare; Medicaid, which is funded through the second quarter of fiscal year 2026; CHIP; Federal Marketplace; and healthcare fraud and abuse control will continue. Most survey and certification activities will halt except in the case of serious patient harm investigations. Contract awards and “other obligation types using discretionary funding” are also suspended.
- CDC: A total of 4,111 CDC and Agency for Toxic Substances and Disease Registry staff are retained, with 1,784 exempt due to their positions being already funded or otherwise exempt and 2,327 who are excepted due to their positions being “deemed necessary by implication.” Disease outbreak response, the President’s Emergency Plan for AIDS Relief, the World Trade Center Health Program, the Energy Employees Occupational Illness Compensation Program Act, and Vaccines for Children continue. However, activities suspended include guidance to state and local health departments, public health communications, applied public research, surveillance data analysis, public inquiries, and grant funding announcements.
- NIH: A total of 5,283 NIH staff, or 31.53%, are retained and excepted, with no NIH staff classified under the exempt category. The Clinical Center operates at around a 90% capacity and continues care for existing patients, admitting new patients only when medically necessary. Halted activities include grant peer review meetings, advisory council meetings, new awards, new protocols at the NIH Clinical Center, basic and translational research, training programs at NIH facilities, scientific meetings, and most administrative functions.
- FDA: All 16,089 FDA staff continue normal operations through Sept. 30, due to full-year appropriations.
2. Shutdown disrupts hospital at home. The legislative package includes key healthcare provisions backed by hospital and provider groups, including an extension of pandemic-era telehealth flexibilities through 2027. It also extends the waiver for CMS’ hospital-at-home program through 2023.
In the meantime, the partial shutdown has disrupted hospital-at-home programs, as even temporary waiver lapses require hospitals to pause services to remain in compliance with federal rules.
“It takes weeks to plan for a shutdown and weeks to turn the program back on,” Constantinos “Taki” Michaelidis, MD, medical director of UMass Memorial Health’s Hospital at Home program, told Becker’s. “With Hospital at Home, when we lose the waiver, if we still have patients with us, it becomes a compliance issue. We would be in violation of Medicare Conditions of Participation if a patient is still on service at 12:01 a.m. Saturday morning [Jan. 31].”
3. DHS funding faces holdup. The House initially passed a six-bill funding package Jan. 22, and the deal was widely expected to advance through the Senate. However, momentum stalled after federal immigration agents fatally shot 37-year-old registered nurse Alex Pretti in Minneapolis on Jan. 24. In response, Senate Democrats said they would move DHS funding forward without reforms to immigration enforcement operations. The impasse prompted Democrats to push for separating DHS funding from the broader package. Lawmakers eventually agreed to move forward on a revised deal that funds five agencies through Sept. 30 and provides a two-week extension for DHS.
Editor’s note: Naomi Diaz contributed to this report.
