In the wacky world that is Washington, contradictions, irony, and paradox are sometimes the norm. So maybe no one inside the Beltway should be surprised by a new proposal from the House of Representatives.

A proposal by the Republican-controlled House would reduce the FDA’s FY 2011 budget request of approximately $2.5 billion by $220 million to $2.28 billion. That number represents a $78 million reduction from actual FY 2010 spending—a big number for FDA.

Roughly $1.5 billion in the proposed budget comes from user fees; about $250 million of which have not been authorized (See “The Pink Sheet” DAILY story). Currently, agencies are allowed to spend at fiscal 2010 levels under a continuing resolution that ends March 4.

The new Republican leadership in the House has been previewing across-the-board budget cuts since the party’s victory in November. What took many FDA stakeholders by surprise is the size of the cut.

The proposed cuts are a large number for FDA, an agency that has been chronically underfunded to meet its rapidly expanding authorities and responsibilities.

Now stakeholders are wondering, if the cuts were to go through, what areas at FDA would be hardest hit.

“This would be prorated across existing appropriations. So for drugs, generics and foreign inspections in particular would be hard hit. Also drug safety,” says one official.

Cuts that big would almost certainly impact FDA operations across the board. If enacted, newer initiatives such as the food safety authorities, tobacco, and FDA’s regulatory science push would likely be at highest risk. FDA’s Sentinel active surveillance initiative also would be an area that could lose resources.

Democrats on the House side appeared surprised by the $78 million reduction and few had figured out exactly which FDA operational programs would be targeted.

On the drug/generic/medical device review side, the budget reductions would tilt some leverage toward regulated industry in ongoing user fee negotiations as the agency could be more dependent on private sector dollars.

Nevertheless, it would be hard to see a scenario where new drug, generic, and medical product review times aren’t substantially increased in the future if the agency’s budget is shrunk by the magnitude the House leadership is proposing.

“A significant cut like what is being proposed will hinder the agency’s ability to fully implement recently-established programs. This problem of adding responsibilities without sufficient resources is one that for years has eroded the scientific capacity of the agency, which directly impacts new treatments getting to patients,” said Ellen Sigal, Chair of the patient advocacy group Friends of Cancer Research.

Both Republicans and Democrats have long lamented the lack of funding from appropriations for FDA. The new budget proposal would only make the problem worse.