The debt deal struck by leaders in Washington last week has food policy insiders worried about the future of food safety funding at both the U.S. Department of Agriculture and the Food and Drug Administration.

The deal — liked by virtually no one, but praised for saving the country from default — raised the debt ceiling through 2012 in exchange for between $2.1 and 2.4 trillion in savings over the next 10 years, including $917 billion in savings by capping discretionary spending, which includes public health agencies.

Future budget cuts, though significant, will “protect core investments,” according to the Obama administration, but it is hard to see a budgetary scenario in which FDA and USDA, and the Centers for Disease Control and Prevention, are able to expand their capacity or invest in additional initiatives. Appropriators in the House and Senate have tough decisions ahead as they work to trim almost a trillion dollars from a wide variety of programs.

The spending limits come right as FDA is working to implement an ambitious food safety overhaul, mandated by the FDA Food Safety Modernization Act that President Obama signed into law in January.

“I don’t see [FDA] going above flat line at best … which is effectively a cut,” says food safety consultant David Acheson, who served as associate commissioner of foods at FDA under the Bush administration. “FDA will likely stay on track with the [Food Safety Modernization Act] rule writing, but enforcement will be compromised as will the inspection mandates.”

The Alliance for a Stronger FDA, a group of consumer and industry interests that lobbies for building the agency’s capacity to regulate food and drugs in the 21st century, says it’s “impossible to say” where exactly FDA or other agencies stand before the appropriations subcommittees weigh in, but the agency would likely fare better than under the House-passed agriculture appropriations bill. The House measure called for $285 million in cuts to the agency for fiscal year 2012, an 11 percent cut, $87 million of the reduction would come from food safety.

The Alliance is continuing to actively lobby for a budget increase at FDA and is planning an ad campaign targeting Capitol Hill publications in September.

“We have been active in presenting the Senate with reasons why FDA needs an increased level of funding in FY 12,” writes Steven Grossman, deputy executive director for the Alliance. “We have been working to show the House that a higher FDA number from the Senate would be justified and should be accepted.”

“FDA’s responsibilities are not going to shrink just because federal spending is being reduced. We hope Congress sees, as we do, that FDA is not optional,” added Grossman. “It is part of what society needs to function.”

How the debt deal will impact USDA programs, including the Food Safety and Inspection Service, is also not entirely clear. Though the deal stipulates what cannot be cut — food stamps and direct payments, for example, are protected through at least 2013 — discretionary cuts will still apply.

“We’re not sure how they’re going to allocate these discretionary cuts, but clearly, you know, the department’s going to get their share, and they’ve been cut so much already that it’s going to have an impact,” Rep. Collin Peterson (D-MN), ranking member of the House Agriculture Committee, told in an interview last week.

Agriculture Secretary Vilsack told an audience of food protection professionals in Milwaukee he would work to keep food safety a priority at USDA.

“There are a lot of things we’d like to do, but one of the things we must do, and I will tell you that food safety is one of those things that … is a must do,” said Vilsack at the International Association of Food Protection conference last week, citing the tough budget landscape ahead. “We’ll be looking at ways in which we can, even in a constrained resource environment, do a better job.”

The House agriculture appropriations bill, passed in June, calls for a $35 million cut, a less than 4 percent cut for meat, poultry, and processed egg inspection. The Senate has not acted on FDA and USDA budgets for FY 2012 yet.

As for the more structural spending cuts under the debt deal, a so-called super committee made up of six Democrats and six Republicans will ultimately outline the toughest reductions — entitlement reform, tax reform and revenue are all on the table, though what combination of these will be tenable is not clear. The panel must develop a plan to reduce approximately $1.5 trillion in deficit reduction over ten years and report back by Nov. 23.

If the committee fails to find cuts, or Congress refuses to adopt them, an enforcement mechanism will trigger spending reductions beginning in 2013 – split 50/50 between domestic and defense spending, according to the White House outline of the agreement.

Enforcement protects Social Security, Medicare beneficiaries, and low-income programs from any cuts, but the triggers could have significant impacts on other domestic programs, including food safety and other public health functions.