Before the sun came up in Washington, DC Saturday the House passed a continuing resolution–with $61 billion in budget cuts–to fund the government from March to September. Key food safety agencies, including the U.S. Food and Drug Administration, the U.S. Department of Agriculture’s Food Safety and Inspection Service and the Centers for Disease Control and Prevention would take substantial cuts under the plan.

According to the original House proposal, $222 million would be cut from FDA, $53 million from FSIS, $755 million from CDC, $336 million from the National Oceanic and Atmospheric Administration (NOAA)–an agency that is playing a major role in testing Gulf seafood for chemicals in the wake of the BP oil spill–and $246 million from the Agriculture Research Service, the research arm of USDA. All of the estimated cuts are based on President Obama’s FY 2011 budget request, which was never enacted.

“We held no program harmless from our spending cuts, and virtually no area of government escaped this process unscathed,” said House Appropriations Chairman Hal Rogers (R-KY). “While these choices were difficult to make, we strived to spread the sacrifice fairly, weeding out waste and excess, with a razor-sharp focus on making the most out of every taxdollar.”

The Alliance for a Stronger FDA noted that FDA took a bigger hit in the second round of budget cuts.

“When the House appropriations committee was asked to find another $24 billion in FY 11 cuts, we knew this would be bad for all federal agencies, including FDA,” said the Alliance in an update Friday.

“Indeed, under HR 1, the current House FY 11 CR, FDA would receive $400 million less than the President’s request and a whopping $242 million below the FY 10 appropriation. No matter how supportive the Senate might turn out to be for FDA’s cause, the House position makes it quite unlikely that the final compromise will provide any growth to FDA. If the House and Senate were to “split the difference,” as is often the case, the second set of House numbers pulls the “middle ground” way down. This is discouraging, but be assured that the Alliance will continue to advocate for the highest possible number for FDA.”

The impact the final version of the legislation would have on FDA, USDA, and CDC will become more clear this week when a clean version of the CR is released.

The Senate, which is not expected to approve the House CR, will take up its FY 2011 CR debate after Congress returns from recess on February 28. The current continuing resolution expires March 4.