Workers at one of Kraft's manufacturers in Illinois turned up a contaminated batch of fruits and nuts in December 2007. Then, in September of last year, another positive sample appeared.
Only after thousands of tests could the company pinpoint the source for the second positive test as California-based Setton Pistachio of Terra Bella, Inc., said Kraft spokeswoman Susan Davison.
Last week, the food products giant recalled or destroyed all suspect foods, and notified its suppliers and the Food and Drug Administration, which on Monday issued a sweeping national warning against eating the nuts.
"If we did detect salmonella, of course we would never ship our products," Davison said. "We conducted extensive testing of all our food, and we were just unable to zero in until March that pistachios were the root cause."
On Friday, Lee Cohen, a production manager for Setton's sister company in New York, said Kraft did not tell Setton until recently that they had detected salmonella-tainted pistachios last year. The company later retracted his statement without explanation.
Setton, the second-largest pistachio processor in the nation, sells its nuts to Kraft and 35 other wholesalers across the country, which use them in everything from ice cream to cake mixes. As FDA officials scour its records and swab its factory, the plant has temporarily shut down after recalling more than 2 million pounds of nuts.
No pistachio-related illnesses have been reported.
Also Friday, the FDA sent out a letter to the pistachio industry reminding nut processors to follow good manufacturing practices to protect consumers, something food safety experts called welcome guidance.
Dr. David Acheson, FDA's assistant commissioner for food safety, said Kraft first told the administration about the problems last week.
Neither federal nor state laws require food manufacturers to test the safety of their products or to report any findings of contamination, though many do if they plan to recall a product, Acheson said.
"If they find problems in a product prior to shipment, they'll pull it back and destroy it," Acheson said. "I wouldn't call that a good manufacturing practice, but that is clearly a good public health practice."