The Obama administration is requesting cuts at most agencies in its 2014 budget, released on Wednesday, but seeking a significant increase in funding at the U.S. Food and Drug Administration to help the agency implement the monumental Food Safety Modernization Act.

While the administration’s budget is very unlikely to be enacted, it underscores the White House’s priorities and outlines a starting point for the future debate over spending levels for the agencies.

The White House proposed $3.8 trillion in spending for fiscal year 2014, including $4.7 billion for FDA, which represents a more than 20 percent increase over its 2012 budget. More than 90 percent of the $821 million boost would come from industry user fees.

For food safety, the administration is proposing a $295 million increase, compared to FY 2012, to “build a strong, reliable food safety system,” but only $43 million of that increase would be regular funding. More than $252 million of it would come from food facility registration and inspection fees and food importer fees, but it’s not clear that Congress will actually mandate those fees for the food industry.

According to the budget breakdown from the White House, legislation will be proposed to allow FDA to collect fees for food facility registration and inspection as well as for food import to implement the requirements of FSMA. The document says $59 million would come out of registration and inspection fees. On the import side, the administration estimates it would collect $166 million to support food safety efforts. The food industry has long argued against user fees.

“These are tight budget times, and the FDA budget request reflects this reality,” said FDA Commissioner Margaret Hamburg. “Our budget increases are targeted to strategic areas that will benefit patients and consumers and overall strengthen our economy. Through the good work of the FDA, Americans will receive life-saving medicines approved as fast as or faster than anywhere in the world, confidence in the medical products they rely on daily, and a food supply that is among the safest in the world.”

Sandra Eskin, project director of the Food Safety Campaign at The Pew Charitable Trusts, said the group was pleased to see additional appropriated funds included in the proposal.

“We will look closely at the fee proposals and work with other stakeholders to assess their viability,” she said.

USDA and CDC

The Obama administration proposed reductions at the U.S. Department of Agriculture and the Centers for Disease Control and Prevention, but food safety programs were not particularly targeted.

The budget proposes a little over $1 billion for USDA’s Food Safety and Inspection Service, giving the agency nearly $4 million more than its 2012 spending level, but $2 million less than the current continuing resolution. The budget proposes a performance-based user fee “which will be charged to plants that have sample failures or require additional inspection activities due to regulatory non-compliance.”

The FSIS budget also notes that there is a spending decrease for “implementation of new methods of poultry slaughter inspection,” referring to the controversial HACCP-Based Inspection Models Program that restructures poultry inspection and reduces the number of FSIS inspectors in each plant doing physical inspections of the birds.

Wenonah Hauter, executive director of Food & Water Watch, criticized the budget, saying that it paved the way for “an ill-conceived proposal to remove government inspectors from slaughter facilities and turn over their responsibilities to company-paid employees.” Food & Water Watch contends that quality defects and serious food safety concerns like fecal contamination are missed more often in plants that participate in HIMP.

Both FSIS and the poultry industry argue that HIMP improves food safety by focusing FSIS inspectors on critical food safety tasks, like sampling for pathogens, instead of doing quality control tasks in plants.

Ashley Peterson, National Chicken Council vice president of scientific and regulatory affairs, noted the debate over HIMP has been “a long-running battle between the department and the inspectors union,” and said it was unfortunate that “the union and their allies have been slinging mud and inaccuracies about the proposal and our industry in order to save taxpayer funded jobs that have proven unnecessary for more than 13 years.”

Under the administration’s proposal CDC would take a significant $270 million cut, but some areas, including “emerging and zoonotic infectious disease activities” are singled out for increases. For example, the budget asks for $40 million for a new initiative to improve CDC’s technology for tracking and solving disease outbreaks.

According to CIDRAP, CDC Director Tom Frieden said the initiative – the Advanced Molecular Detection and Response to Infectious Disease Outbreaks – would “allow us to find outbreaks quicker, to find a higher proportion of outbreaks.”

The effort, CIDRAP noted, is being developed in response to a 2011 report from an external panel of experts, who “identified a number of critical gaps in CDC’s surveillance capabilities and starkly concluded that CDC was on the path to becoming obsolete, if not irrelevant.”

The White House FY 2014 budget proposal can be viewed here.

This article has been updated.