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."
Kraft finally determined pistachios caused last year's problem in March, when their manufacturer in Illinois detected salmonella for the third time - this time in the nuts, the only common ingredient between the second and third batch of trail mix, Davison said. Kraft has not traced the source for the first positive salmonella test in 2007.
Salmonella, the most common cause of food-borne illness, causes diarrhea, fever and cramps. Most people recover, but the infection can be life-threatening for children, the elderly and people with weakened immune systems.
Roasting is supposed to kill the bacteria in nuts, but problems can occur if the roasting is not done correctly or if roasted nuts are re-contaminated. That can happen if mice, rats or birds get into the facility.
Setton Pistachio officials suspect the roasted pistachios sold to Kraft Foods may have become mixed at the plant with raw nuts that could have contained traces of the bacteria.
Cohen, the production official at Setton International Foods Inc. in Commack, N.Y., said Friday that Setton Pistacio's internal tests had detected salmonella on some of its raw pistachios in the past, but said all tainted pistachios were later roasted. He did not specify when those tests were performed.
"We have found salmonella on raw pistachios, but that doesn't mean anything because those nuts are coming straight from the orchards where you could have had a very small localized contamination from birds," Cohen said. "Those nuts never hit the marketplace."
More than a dozen other companies that got their nuts from the California plant have recalled their pistachio products this week for fear of possible contamination. On Friday, Setton International announced it was also voluntarily recalling about 118,000 pounds of pistachio products.