The U.S. Food and Drug Administration, responsible for 80 percent of the food supply, is halting routine food inspections. This means no government oversight of practically everything else in the grocery store. Also, most of the experts at the Centers for Disease Control and Prevention, the group that identifies and tracks foodborne illnesses, have been told to stay home.

“Make no mistake: The safety of our food supply will suffer if agreement is not reached on a continuing resolution that funds the government,” says Caroline Smith DeWaal, director of food safety at the Center for Science in the Public Interest, a longtime food safety advocate.

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“The government’s food safety functions are far more pressing than the unrealistic demands being made by petulant extremists in the House.”

The situation at FDA seems critical. The agency is maintaining 55 percent of its 14,779 employees while in shutdown mode, but this includes workers who focus on drugs, tobacco and other nonfood areas, many of which have budgets propped up by industry user fees.

Remarkably, the shutdown plan is more generous than the outline floated in 2011, the last time the federal government was facing the brink. Under that plan, the administration deemed only 14 percent of FDA’s workforce essential.

Still, food safety advocates are very concerned about the direct hit to food safety.

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Ceasing routine food inspections is not ideal, experts say, especially because FDA is already so short-staffed compared with the size of its jurisdiction. During the 2012 fiscal year, the agency inspected about 10,000 of the 167,000 domestic food manufacturers. Overseas, it was able to get into 1,300 of the 254,000 food facilities registered with the agency.

According to the plan released by the administration, FDA will be “unable to support the majority of its food safety, nutrition, and cosmetics activities.” That includes routine food manufacturer inspections, compliance and enforcement of food safety regulations and food import monitoring.

When it comes to the CDC, which is operating with 32 percent of its 12,825 employees during the shutdown, health experts worry the disease surveillance system for detecting foodborne illness could be hampered by the loss of personnel.

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While the public learns of maybe only a dozen high-profile national foodborne illness outbreaks each year, at any given point there are dozens of clusters of illnesses tied to food and investigators try to pinpoint the cause.

CDC’s PulseNet — a crucial part of the agency that tracks and monitors foodborne illnesses across the country — has been hit hard by the shutdown. Each year, PulseNet monitors 250 clusters of foodborne disease and only 10 to 15 get high-profile media attention.

“CDC will continue minimal support to protect the health and well-being of U.S. citizens here and abroad, including continuing to operate PulseNet, CDC’s foodborne disease tracking system,” said Barbara Reynolds, a spokesperson for the agency.

The agency is currently tracking more than 30 clusters of illnesses, but under the shutdown CDC has just one person instead of eight monitoring important pathogens such as Salmonella, E. coli and Listeria, and another person monitoring Listservs and data systems to inform of outbreaks and investigations — a job usually done by five people.

“The long and the short of it is that there is only a skeleton crew at CDC to respond to any kind of outbreak,” said Scott Becker, director of the Association of Public Health Laboratories. “It’s awful for public health.”

The group’s food safety director, Shari Shea, noted that during the shutdown there “isn’t going to be anyone working to figure out what food made people sick and get it off the shelves.”

“You can only do so much with a skeleton staff,” Shea said.

Joseph Corby, executive director for the Association of Food & Drug Officials, said he worries that if a major outbreak or recall occurs during the shutdown, public health could be jeopardized.

“If there’s a big illness, big recall, we work very well as a team,” Corby said. “But under the shutdown, they’re going to have less resources, which is where it gets a little concerning. It’s kind of like we’re keeping our fingers crossed.”

Chris Waldrop, director of food policy at Consumer Federation of America, agrees that emergency responses will be limited at both FDA and CDC. “It’s the exact opposite of what we want to see,” he said.

Less effected by the shutdown is the Food Safety and Inspection Services, the agency within the Department of Agriculture tasked with monitoring meat and poultry. It will be operating with 87 percent of its 9,633 employees, essentially keeping all federal meat and poultry inspectors on the job.

But the USDA warns in its plan that “certain headquarter functions can be suspended for a very short time without a direct and immediate impact on the safety of human life. A lengthy hiatus would affect the safety of human life and have serious adverse effects on the industry, the consumer and the agency.”

The shutdown of nonessential programs can still have a dramatic effect on manufacturers. For example, Corey Henry, a spokesperson for the American Frozen Food Institute, which represents hundreds of food companies, said that while the association has been told USDA inspections will not be halted, the group is concerned about the serious slowdown for food label approvals.

USDA has to greenlight all labels for meat products before they can hit the market. The staff that reviews the labels is considered nonessential.

“This is an issue we will monitor closely, as further delays in food product labels could significantly impact frozen-food makers,” Henry said.

“Farmers depend on these agencies,” said American Soybean Association President Danny Murphy. “Whether it’s the county Farm Service Agency office, staff at the Risk Management Agency, market access work done by the Foreign Agricultural Service or Office of U.S. Trade Representative, or the work done at the Agricultural Research Service, soybean farmers have a long-standing and valuable working relationship with our federal partners at USDA, and their absence for the foreseeable future will be painfully apparent.”