Early 2011 was a time of intense pressure inside the A.T.F. The agency was under fire from Congress over the Fast and Furious operation, in which agents allowed gun traffickers to buy weapons and ship them to Mexico, hoping the shipments could lead them to major weapons dealers. Justice Department auditors began scrutinizing how A.T.F. agents managed their tobacco smuggling investigations.

With that audit continuing, the A.T.F. issued new rules to tightly monitor undercover investigations. Soon after those rules went into effect, U.S. Tobacco completed its purchase of Big South for $5.5 million, a deal that gave Big South the authority to buy and sell cigarettes on behalf of the cooperative. Almost immediately, the farmers say, Mr. Carpenter and Mr. Small began defrauding them.

It worked like this: An export company working with the A.T.F. placed an order for cigarettes to be shipped internationally — thus not subject to American taxes. Big South would instead ship bottled water and potato chips, making it look as if cigarettes had been exported. Mr. Carpenter and Mr. Small would then buy the tobacco at a slight markup through a private bank account. Lastly, they would sell the tobacco to Big South, again at a markup.

Because they had the authority to buy on behalf of the tobacco cooperative, “Carpenter and Small simply sold products to themselves,” the farmers wrote in court documents. All of these transactions occurred on paper. The cigarettes never left the Virginia warehouse.

“It’s what I saw with my own eyes,” said Brandon Moore, the warehouse manager and one of the people who discussed the transactions in the case. Their accounts fit with descriptions in court records.

Mr. Moore said he was aware of the A.T.F. operation but became troubled by it as he learned more. “It shouldn’t be going on, even if it is the A.T.F.,” he said.

In one deal described in the lawsuit, the informants bought tobacco at $15 a carton and sold it to U.S. Tobacco at $17.50. The profit, about $519,000, went into what was known as a “management account.” That account, while controlled by Mr. Carpenter and Mr. Small, helped pay for A.T.F. investigations.