The Department of Justice charged Stewart and Michael Parnell, who controlled the now-bankrupt Peanut Corporation of America, and two former PCA employees with knowingly distributing salmonella-tainted peanut products and obstructing the official investigation of the outbreak.
The department said the Parnells and former Georgia PCA plant manager Samuel Lightsey for years had hidden from buyers the fact that their peanut products, used in many popular consumer foods, carried the bacteria salmonella, which can cause severe cramps and diarrhea and in extreme cases lead to death.
It said they fabricated the results of food-safety inspections and analysis to demonstrate to buyers their products were safe, when inspections had shown the presence of salmonella and also when no inspection had been done.
Even after the outbreak of salmonella was traced to peanuts, the department said, the company tried to hide the presence of the bacteria in its products.
The 76-count indictment released Thursday included charges of violation of US food safety laws, obstruction of justice, and mail and wire fraud. A fourth PCA employee, Mary Wilkerson, was charged with obstruction.
The department said the company's plants had a history of chronic unsanitary conditions that led to the frequent presence of salmonella.
"When food or drug manufacturers lie and cut corners, they put all of us at risk," said the US principal deputy assistant attorney general, Stuart Delery.
"The Department of Justice will not hesitate to pursue any person whose criminal conduct risks the safety of Americans who have done nothing more than eat a peanut butter and jelly sandwich."
PCA filed for bankruptcy within months of the outbreak after being forced to shut its plants.
Meanwhile on Thursday the Food and Drug Administration recalled pet treats manufactured by Kasel Associates Industries for potential salmonella contamination.
The FDA said its inspections had found more than 10 different salmonella species in the company's products and facilities.
"While there are no reports of human illness, FDA has received a small number of complaints of illness in dogs who were exposed to the treats."