In a tough budgetary climate, the U.S. Food and Drug Administration received essentially the only increase in an agriculture appropriations bill that advanced in the Senate this week, just as the agency works to implement the Food Safety Modernization Act.

The bill, approved by the Senate Appropriations Committee Wednesday, provides more than $350 million more for FDA and $35 million more for the U.S. Department of Agriculture’s Food Safety and Inspection Service than the House appropriations bill. The Senate bill boosts FDA’s budget $50 million and keeps FSIS’ budget flat compared to fiscal year 2011 — an impressive feat as programs across government agencies sustain significant cuts.

“These cuts are real and are difficult to implement, but that is the will of the Congress and the charter of this Committee,” said Appropriations Chairman Daniel Inouye (D-HI), during mark up of the ag budget bill. “Together with the funding reductions approved for fiscal year 2011, the Congress has cut the Administration’s request for these two years by more than $157 billion. This makes our funding recommendations the largest reduction by Congress of any President’s requests in history over this two year period.”

According to the Committee, the funding level set in the bill prioritizes health and safety considerations in the face of a stark budget reality. Most programs took a 5 percent cut.

FDA’s funding level, for example, “takes into consideration the federal government’s responsibilities to protect public health and safety, especially in the areas of food, drugs, medical devices, and biologics. An increase is provided to the Food and Drug Administration to begin implementation of the recently passed Food Safety Modernization Act,” according to the Committee’s budget summary.

Food safety and FDA advocates were thrilled by the development.

“We are grateful for Senate leadership to assure 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 in a statement. “At a minimum, we urge the House to accept the Senate levels and we ask conferees to consider whether any additional funds can be made available.”

Wenonah Hauter, executive director at Washington, DC-based Food & Water Watch, also praised the move and called on Congress to find more resources for FDA.

“It’s encouraging that the Senate bill does not include the cuts to FDA’s food safety program that are found in the House version, but the agency will still need even more resources to be able to meet its new responsibilities, especially increasing inspections of domestic and foreign food processing establishments,” said Hauter in a statement Wednesday.

“As the appropriations process moves forward, we urge members of Congress to make sure that USDA and FDA have the resources they need to protect public health with strong food safety programs. The Senate version of the appropriations bill for FY 2012 provides those resources and these funding levels should be adopted by the full Senate and the conference committee.”

The increased focus on food issues — in the wake of massive recalls, foodborne illness outbreaks, and rapidly growing food imports — has led to a broad effort to reform the food regulatory system, but many in the food policy realm have been concerned about funding for new programs.

“We count on FDA to continue to make sure our foods are safe, regardless of origin,” said John Connelly, an Alliance Board Member and president of the National Fisheries Institute.  “As Americans enjoy more foods from overseas, the agency must invest several times more effort in import safety than it has in the recent past.”