Congress’s inability to pass a long-term spending bill has major ramifications for public health, advocates and former agency officials warn.

The short-term measures hinder efforts to play ahead and recruit staff even as they keep the government open, the advocates say. They have left public health agencies “treading water,” said Ellie Dehoney, vice president of policy and advocacy at Research!America. “It’s just a state of suspended animation.”

Congress passed its fourth stopgap measure in nearly four months on Monday after a brief shutdown, and more could be on the way. The measures, known as continuing resolutions, keep government spending consistent at current levels, but leave agencies facing uncertainties over their long-term budgets.

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State and local agencies — like health departments — rely on federal funding and grants from agencies such as the Centers for Disease Control and Prevention (CDC) and the National Institutes of Health.

These dollars help perform research and other missions vital to a community, such as responding to an outbreak of a foodborne illness or the flu, treating sexually transmitted diseases or opioid addiction and contracting out these and other critical services.

Without certainty over that funding, they can’t plan ahead.

“You end up with instability at the fundee level — at the local or state health department or community agency level — because you have no continuity in terms of the funding you receive,” said John Auerbach, president and CEO of Trust for America’s Health. He’s also a former CDC official who worked as a city and state health commissioner.

“States and localities are stuck in neutral waiting for clarity,” said Ed Hunter, CEO of the de Beaumont Foundation and former director of the CDC’s Washington office under President Obama.

Repeated short-term funding bills also limit the ability of federal agencies to hire and train new employees.

Government researchers and scientists may choose to work in the private sector, where the pay is better and there isn’t a threat of a government shutdown — which could harm ongoing research projects.

“The shakiness of the system itself sends a really bad signal,” Dehoney said. “It’s not the way to do business.”

“It’s very hard to attract the best and brightest to government when you can’t offer them stability, or sanity, for that matter,” Hunter said. “I do think it’s hard to measure, but there’s a clear cost in productivity when you’re on this stop-and-start” that comes from continued short-term funding bills.

Long-term research may also be delayed.

“If you are in one of the research programs, it's very difficult to start a long-term research project again if you don’t know what that funding stream is going to be, so it holds up requests for proposals, requests for ideas,” said Georges Benjamin, the executive director of the American Public Health Association.

The uncertainty throws a wrench in planning for emergencies. Agencies don’t know how much money public health agencies will have to pay staff’s salaries, purchase supplies and more, sources said. And it makes it hard to scale up the resources in the event there’s a public health emergency.

“Imagine a police department that is having to manage with no sense of what their budget is,” Benjamin said. “If something happens, they can’t hire more police officers. They are unlikely to do things that are needed but not absolutely essential.”

Jeff Allen, CEO of the advocacy group Friends of Cancer Research, said public health agencies need flexibility to rapidly move funds around in the case of an emergency, or a new breakthrough treatment. The funding restrictions of continuing resolutions make that nearly impossible, he said.

Following a three-day shutdown, Congress passed a short-term spending bill Monday that goes through Feb. 8, and included six years of funding for the Children’s Health Insurance Program.

But the legislation didn’t reauthorize other health programs that expired on Sept. 30 — such as a pot of money for community health centers — which is also having an impact across the country.

“All of these major federal programs play a significant role in the work of state and local health departments, and without certainty around budget and continued sustainability, we are looking at freezes to program enrollment, scaling back of services, and potential layoffs at the local and state levels,” Michael Fraser, the executive director of the Association of State and Territorial Health Officials, wrote in an email.