Editor’s note: This column includes information from an “Advocacy at a Glance” posting by the Alliance for a Stronger FDA and analysis and commentary by Steven Grossman, deputy executive director of the alliance, both republished here with permission.

President Donald Trump is proposing shifting $54 billion from domestic to defense programs in fiscal year 2018, which begins Oct. 1.

The proposal, unveiled in a speech to Congress on Feb. 28, calls for an approximate 10 percent increase for defense programs and an approximate 10 percent cut for non-defense discretionary programs. At this point we have no indication how the Food and Drug Administration would be treated in the president’s proposal. However, for reference purposes, a 10 percent cut in FDA’s appropriation would mean a loss of $272 million in program funds and take FDA back to approximately its FY 2012 level.

A number of non-defense programs are likely to be protected in the President’s proposal, such as veterans’ programs and border security. Thus, to pay for the defense build-up, the president’s proposal could well include cuts for non-protected programs that are closer to 12 percent to 14 percent. The percentage could be even higher if the president proposes that non-defense programs be cut further in order to pay for proposed new initiatives, such as the border wall or rebuilding our nation’s infrastructure.

While Congress has final say on appropriations, FDA stakeholders should be very concerned, but not panicked. What the president described is just a general proposal, to be fleshed out with more details when he sends his budget outline to Congress in mid-March and his complete budget proposal in late April or May. Congress will make the final decisions. However, regardless of the actual numbers in the president’s proposal, the tone and direction threatens FDA’s appropriation and the agency is at risk. We need to advocate for FDA to be one of those protected programs that are not subject to a 10 percent to 15 percent cut because they are considered a national priority.

As described in the Feb. 24 Analysis and Commentary from the Alliance for a Stronger FDA, there are really only two ways to pay for a defense build-up: take the monies from non-defense programs —   mandatory or discretionary — or increase the federal deficit, which is very unlikely.

Thus, we are likely into a “guns vs. butter” fight this year, with strong policymaker sentiment in both directions and most members of Congress yearning for a way to avoid choosing. Congress thought it settled this question through FY 2023 when it passed the Budget Control Act of 2011, creating a decade’s worth of budget caps specific to defense and non-defense spending. While the Alliance will not be taking sides in this larger battle, the downward pressure on all non-defense programs will be enormous. There is no question that FDA is at risk.

What the President must decide — in his budget outline before mid-March and then reinforce or modify in the full budget request by late April-May — is into which of three buckets to assign every non-defense federal program. The first bucket will contain programs slated for larger cuts based on policy or ideology. The Environmental Protection Agency (EPA) is clearly going to be in this bucket, as will foreign aid programs and support for the arts and humanities.

The second bucket will contain programs slated for an average cut — think 10 percent to 15 percent, probably across-the-board — in order to generate the monies necessary to pay for defense and for which the Administration sees no justification for giving special treatment. The bulk of federal programs will be in this second bucket.

The third bucket will be a select group of programs for which the Administration will be advocating for a smaller cut, level funding or possibly an increase. I anticipate this bucket will include the FBI, border security, veteran’s programs and maybe air traffic controllers.

Relative to the Trump Administration, the Alliance’s primary goal will be to advocate and show the justification for FDA being placed in the third bucket. This would not only benefit us in having a higher baseline in the president’s request, but would also send a strong message to Congress that FDA is a priority, whose portfolio of activities represent core functions of government.

Getting into the third bucket is going to be a tough sell with a new Administration that hasn’t yet figured out what it thinks about FDA. Further, the process makes such advocacy almost impossible.

The initial budget guidances were sent by OMB to departments only the first week of March. It is unclear whether HHS is following the traditional pattern of sending allocations to agencies and entertaining appeals. Even if so, there will not be a lot of time for back-and-forth discussions with agencies, given the apparent time constraints. FDA’s fate in the Trump budget will truly be in HHS’s hands. While Congress will have the final say, it would be invaluable if the Administration would lead the way in recognizing FDA “exceptionalism.”

Regardless where Congress ultimately nets out on defense increases vs. non-defense cuts, the environment for funding increases for non-defense programs is going to be difficult. We need to be steadfast in our message that individualized, policy-driven consideration of agency missions and responsibilities should be the key to appropriations process, rather than across-the-board decisions.

We hope the current process, Congress and the Executive Branch, will allow for this. If that happens, we believe that FDA is a unique agency with unique responsibilities and can justify its current funding level or even the small increase that the Alliance is requesting.

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