Lawmakers have until Dec. 11 to pass an omnibus bill for fiscal 2016, and with extra money made possible by last month's budget deal, HHS and the National Institutes of Health could see extra funding.
If they cannot get an omnibus passed, there could be another continuing resolution agreement to keep funding for a period of time. Otherwise, the government will shut down.
Analysts said lawmakers will add riders to the bill that will be the focus of negotiations and familiar disagreements and could impede a final agreement.
The budget deal raised the sequester caps by $80 billion in the next two fiscal years. For fiscal 2016, $50 billion of that is available and half will go to defense spending.
David Reich, senior policy consultant with the Center for Budget and Policy Priorities, said a shutdown is possible but an omnibus agreement is also not an unreasonable hope. A continuing resolution wouldn't solve much.
“It's a problem for agency operations to not know what their budget is well into the fiscal year,” he said.
Ellie Dehoney, vice president of policy for Research America, said a path to repealing the medical device tax, although it has received some bipartisan support, has not been forged.
It could be tied in with efforts to repeal the “Cadillac” tax on high-end health insurance plans but nothing concrete is in the works for that yet either, she said.
Reich said the extra money could go to departments throughout HHS, but lawmakers may get stuck on issues such as financing for the Affordable Care Act, some research agencies and Planned Parenthood.
The House appropriations bill calls for rescinding past funding of the ACA and eliminating most new spending. It would get rid of Title X family planning funds and also essentially eliminates the Agency for Healthcare Research and Quality and the Center for Medicare and Medicaid Innovation, he said.
Those provisions would be mostly unpalatable for Democrats and the White House, Reich said.
Dehoney said the NIH is likely to get more money than in previous years and it will probably not be earmarked but be used to bolster ongoing research.
“I think it will lift all boats,” she said
The original House Labor, Health and Human Services Funding Bill would allocate $71.3 billion to HHS, which is a slight increase from the year before but about $4 billion below the president's budget request for the agency.
It would also give $31.2 billion to the NIH, $7 billion to the Centers for Disease Control and Prevention and $6 billion to the Health Resources and Services Administration. It would provide $3.3 billion for the CMS, which is nearly $1 million below the president's request.
Dehoney said the budget deal has changed the game, however.
“They're definitely renegotiating all of this because they have extra money,” she said.
In 2013, a government shutdown over implementation of the ACA stalled medical research and FDA drug approvals.