Congress released a compromise bill late Monday that would give the U.S. Food and Drug Administration $2.5 billion for fiscal year 2012, a remarkable $50 million increase at a time many lawmakers are zeroed in on slashing funding.

The compromise gives FDA $334 million more than the spending level approved by the House in June. The increase is directed at implementing the new food safety law and advancing bioterrorism response.

The bill also gives $1.0 billion for the U.S. Department of Agriculture’s Food Safety and Inspection Service to maintain its current workforce, which is more than $32 million over the House proposal.

Food safety advocates and industry groups, who formed a broad coalition to lobby for increased funding at FDA, were pleased with the conference report.

“We are grateful to the conferees for assuring that FDA has the funds to continue its mission,” said Nancy Bradish Myers, President of the Alliance for a Stronger FDA and President of Catalyst Healthcare Consulting. “FDA must continue to be a national priority so that we can advance medical progress, improve patients’ lives, and assure Americans have a safe food supply.”

Food safety fared well considering the $19.8 billion agriculture bill cut $350 million out of agriculture agencies, which is $4.6 billion below President Obama’s budget request.

“Overall, we’re very relieved that FDA was spared any cuts this year,” said Caroline Smith DeWaal, food safety director at Center for Science in the Public Interest. “They certainly don’t have the full amount that the administration requested, but they have the seed money they need to start implementation.”

Agricultural research, however, did take a substantial hit. The agreement reduces USDA’s research budget by $53 million.

“While trimming spending, this funding level will support research on critical agricultural issues, including emerging crop and livestock diseases, food safety and water quality, and maintains the nation’s investment in land-grant and other agricultural colleges and universities,” according the House appropriations summary.

The House is set to vote on the final conference report–which includes other spending bills and a continuing resolution to keep the government funded through mid-December–this week.