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WASHINGTON — A troubled new computer system for the nation’s 6,500 meatpacking and processing plants shut down for two days this month, putting at risk millions of pounds of beef, poultry, pork and lamb that had left the plants before workers could collect samples to check for E. coli bacteria and other contaminants.

Inspectors say that they were forced to use old paper forms to complete some work, but that in many cases it was too late. “Management sent out a memo saying to reschedule the sampling of meat,” said Stan Painter, a federal inspector in Crossville, Ala., who leads the inspectors’ union. “But in most cases that meat is now gone. We can’t inspect product that went out the door when the system was down.”

Agriculture Department officials, who acknowledge the system failed nationwide Aug. 8, played down the threat to public safety and insisted the breakdown of the $20 million computer system had not compromised the nation’s meat supply. Neither the Agriculture Department nor the meat inspectors could point to any examples of contaminated beef or poultry getting into the hands of consumers.

But Rep. Rosa DeLauro, D-Conn., a longtime food-safety advocate, called the problems with the system “staggering.”

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“Data errors that threaten the health of Americans are unacceptable, and we clearly must do better by American families,” DeLauro said.

The shutdown of the system is only the latest in a series of computer troubles affecting some 3,000 federal meat inspectors who are using the new technology. The inspectors visually and manually inspect every carcass in slaughterhouses throughout the United States and collect samples of beef, poultry and other meats — selected automatically by the new computer system — which are sent to laboratories to be tested for E. coli and salmonella, among other contaminants.

The new inspection system was supposed to be a significant improvement over older methods that the Agriculture Department had used for decades. In the past, food-safety officials at the agency determined which meat would be sampled and at what times. Inspectors collected the samples, filled out paper forms, sent them along with the meat by mail to testing labs and waited days for the results by return mail.

After the new system was set up in 2011, computers set the meat-sampling schedules. Following online directions, inspectors collected specific samples of meat and mailed them for testing to labs. But instead of sending the paperwork along with the meat, inspectors sent information about the samples via the computer system to the labs. The test results were received electronically, and faster than in the past.

The goal was to provide real-time information about the conditions at meat-processing plants and make it easy for the agency to track food-safety problems before they led to outbreaks. “This system allows the agency to be more aggressive and proactive in keeping contaminated products out of commerce,” said Alfred Almanza, administrator of the Agriculture Department’s Food Safety and Inspection Service.

But inspectors say the recent nationwide failure of the computer system — along with other recent breakdowns — undermines the department’s assertions that the new technology has improved the safety of the nation’s meat.

“They’ve poured millions of dollars into this thing, and it still doesn’t work,’’ Painter said.

A report in March by the Agriculture Department’s inspector general found that glitches with the new computer system led to problems with meat sampling at 18 plants last year. At one plant, auditors found that inspectors had not properly sampled some 50 million pounds of ground beef for E. coli for five months. At another plant, which the report identified as among the 10 largest slaughterhouses in the United States, auditors found that computer failures had caused inspectors to miss sampling another 50 million pounds of beef products.

The report did not say whether any tainted meat had reached consumers, but inspectors say it is only a matter of time.

“I was one of the testers on the system in 2010 when it was still in the development phase,” said Jim Shanahan, an inspector from Axtell, Neb. “I sent reports in every day about issues we were having. Today the same problems are still happening.”

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