The ongoing federal government shutdown has stopped most food safety inspections, but the Food and Drug Administration is planning to resume at least some of them. To do it, the agency will have to force furloughed workers to come back without pay.

FDA Commissioner Dr. Scott Gottlieb said he is trying to pinpoint the most essential inspections, while making sure that employees do not suffer too much.

“There’s no question of whether it’s business as usual at FDA,” Gottlieb told NBC News.

“It’s not business as usual, and we are not doing all the things we would do under normal circumstances. There are important things we are not doing.”

This means FDA inspectors are not looking for salmonella in breakfast cereal, E. coli in romaine lettuce, or listeria in ice cream. Companies can still make their own checks, of course, and the FDA is still announcing those recalls.

Foreign food inspections are also continuing, almost as normal, because they’re considered so important. But the FDA has virtually stopped inspecting domestic food production facilities, which could mean threats to the public are going undetected. “We’re doing everything we can to try to maintain our basic consumer protection role. That’s our focus,” Gottlieb said in an interview late Tuesday.

The question of who has to stop operations during a government shutdown depends on funding. Some agencies, including the National Institutes of Health and the Centers for Disease Control and Prevention, got specific funding from Congress last year. But FDA did not.

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Some of FDA’s work, such as drug approvals, inspections of drug-producing facilities, and regulating tobacco products, are paid for by user fees. They’re not greatly affected by the shutdown. But much of the budget is specifically appropriated by Congress, and it’s on hold. About 7,000 of the agency’s 17,000 employees, or 41 percent of staff, are furloughed.

THREAD: Food Safety During Shutdown: We’re taking steps to expand the scope of food safety surveillance inspections we’re doing during the shutdown to make sure we continue inspecting high risk food facilities. 31% of our inventory of domestic inspections are considered high risk — Scott Gottlieb, M.D. (@SGottliebFDA) January 9, 2019

Gottlieb wants to call some of them back to re-start inspections of high-risk domestic facilities. “For me to do that, it would require calling back about 10 percent of our inspection force,” Gottlieb said, estimating the agency employs roughly 5,000 inspectors, making about 160 inspections a month.

“It’s something we currently aren’t doing. I think it’s the right thing to do for public safety.”

The most urgent inspections would be at facilities where there have already been safety issues, such as factories with listeria or salmonella contamination or other hygiene problems. Next comes foods that are more prone to contamination.

“For example, cheese might be a high-risk food,” Gottlieb added. “Low-risk would be a bakery, so a facility that manufactures crackers – that would be low-risk.”

The Center for Science in the Public Interest expressed alarm. “We urge the FDA to publish more information about the impact of the shutdown on the safety of the food supply, including more about which types of inspection, import screening, and enforcement activities are considered critical and which have been suspended,” CSPI’s Deputy Director of Regulatory Affairs Sarah Sorscher said in a statement.

Gottlieb is worried about hurting employees who have been furloughed. He has come up with one creative way to limit out-of-pocket expenses. Food inspectors who travel overseas use credit cards that are billed in their own names, and the staff are reimbursed later by the FDA. Foreign travel can rack up thousands or tens of thousands of dollars in charges quickly, so Gottlieb said he was working to change that billing so it goes straight to the agency.

But there’s another issue for inspectors, many of whom are not paid especially high salaries and who may be living paycheck to paycheck. FDA food inspectors often start at what is known as a GS-5 on the federal government pay scale — a job with a base pay of $30,000 to $37,000 a year.

“We want to protect the public and we will. But I am mindful of the impact that we have on the people of the agency,” Gottlieb said.

Workers who are furloughed can start applying for unemployment benefits, or even find other jobs to fill in while they are idled. They cannot do either if they are called back to work without pay, however. And it is unclear how long this shutdown will last or whether Congress will appropriate back pay for those kept home.

“We are trying to build accommodation in for people who have unusually difficult circumstances,” Gottlieb said.

The FDA takes care of most of the country’s food supply, but meat and some egg products are inspected by the U.S. Department of Agriculture’s Food Safety and Inspection Service. These inspectors are still on the job, the USDA said, but are working without pay. It's because the law, as written by Congress, requires continuous USDA inspection.

CSPI's Sorscher said it is important to consider the impact on staff. “We are concerned about the strain on employees and morale,” she said.

“We don’t want the person inspecting our meat for disease and feces to be distracted by not being able to pay their bills. It is also very hard to get qualified people to work in a slaughterhouse, and many inspectors have advanced food safety or veterinary degrees and could get better-paying jobs elsewhere but choose to work for the government because of the sense of mission and stability,” she added.

“This shutdown could have long-term impacts on our workforce.”