Every year about 130,000 people in the U.S. are hospitalized with a foodborne illness, and 3,000 people die.

To protect against this, the Food and Drug Administration inspects facilities that produce and handle food to ensure safety and compliance with regulations.

But a new report from the Department of Health and Human Services' Office of Inspector General raises some red flags about the inspections program.

"We found a number of weaknesses in the way that FDA is protecting the food supply," Meridith Seife, the deputy regional inspector general, told us.

For instance, FDA often relies on facilities to voluntarily correct violations, which can be ineffective.

Consider this case: Back in 2013, when FDA inspectors went into a facility in Kansas that produces beans and sauces, they uncovered serious problems.

"Inspectors found rainwater leaking through the roof, directly above where food was being prepared," Seife says. "And perhaps most worrisome, the inspection revealed the presence of listeria throughout the facility." Listeria is a pathogen that can cause life-threatening illness.

The FDA issued a warning letter to the facility and requested prompt correction. But the problems were not fixed. "These violations went uncorrected for the next two years," according to the report.

"It is clear that FDA could have done more in this case to have compelled the facility to act more quickly," Seife told us.

Overall, the report concludes that the FDA "consistently failed to conduct timely followup inspections to ensure that facilities corrected significant inspection violations." And in 17 percent of cases, the FDA did not conduct a follow-up inspection at all. Also, in some instances where inspectors found significant violations, the FDA took no enforcement action.

The Food Safety Modernization Act, which was signed into law in 2011, aims to ensure a prevention-oriented approach to food safety. The law gave FDA new enforcement authority so the agency could better respond to problems. But the new report concludes that the FDA has rarely taken advantage of these new tools.

"We think FDA really needs to do more to take swift and effective action" to ensure that safety problems at food facilities are fixed promptly, Seife says.

Officials at the FDA have reviewed the report. The agency's response is included as an appendix. "FDA agrees that there are challenges in its conduct of domestic inspections," writes Lisa Rovin, deputy associate commissioner for public health strategy and analysis at the FDA.

Rovin says that FDA concurs with the recommendations in the inspector general's report, including the need to ensure better use of resources and to take appropriate action against all facilities with significant violations.

In a response from the FDA on Wednesday, a spokesperson said the agency is working as effectively and rapidly as possible to implement the changes brought forth by the Food Safety Modernization Act. She says "our commitment to public health remains strong and unwavering."

Copyright 2017 NPR. To see more, visit http://www.npr.org/.

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