WASHINGTON — The Obama administration is moving to cut down on the thousands of foodborne illnesses linked to chicken and turkey each year with an overhaul of poultry plant inspection rules that are more than 50 years old.

Final rules announced Thursday would reduce the number of government poultry inspectors. But those who remain will focus more on food safety than on quality, requiring them to pull more birds off the line for closer inspections and encouraging more testing for pathogens. More inspectors would check the facilities to make sure they are clean.

The Agriculture Department says the change could cut down on 5,000 foodborne illnesses annually. The changes would be voluntary, but many of the country’s largest poultry companies are expected to opt in. The chicken and turkey industries swiftly praised the new rules, saying they would modernize their businesses.

Federal law requires that government inspectors be present in poultry processing plants. Right now, many USDA inspectors stand in one place on the production line and check for visual defects. This doesn’t do much to ensure the birds are safe to eat, since common poultry pathogens like salmonella and campylobacter are invisible.

The new rules would better train inspectors to find hazards in the plant and would require all companies – whether they opt in or not – to do additional testing for pathogens.

Agriculture Secretary Tom Vilsack said the changes take into account current science, updating the inspection system from 1950s thinking that visual defects meant safety problems.

“This is a significant opportunity to bring the inspection system into the 21st century,” he said.

USDA originally proposed the rule in January 2012, saying the reduction in inspectors would save companies and taxpayers money while also decreasing pathogens in the food supply. Consumer groups have said an overhaul is necessary but criticized the proposal, saying it would shift too much of the inspection burden to the industry.

Those same groups expressed disappointment with the final rule, saying the decreased overall number of inspectors could endanger consumer health.

Wenonah Hauter of the advocacy group Food and Water Watch called it a “gift from the Obama administration to the industry” while Caroline Smith DeWaal of the Center for Science in the Public Interest said USDA “missed the boat” on designing a new system and put budget savings ahead of food safety.

USDA said the number of inspectors at poultry plants could be reduced by around a fourth if all companies opted into the proposal. Some companies – especially smaller ones – may not choose the new system, however, meaning more inspectors would stay in their jobs. USDA said the reductions would mostly come through attrition.

Salmonella and campylobacter are the two top foodborne pathogens that make people sick in the United States. The federal Centers for Disease Control and Prevention estimates that salmonella causes around 1.2 million illnesses in the United States every year, including 450 deaths.