Working from an office suite behind a Burger King in southern Virginia, operatives used a web of shadowy cigarette sales to funnel tens of millions of dollars into a secret bank account. They weren’t known smugglers, but rather agents from the Bureau of Alcohol, Tobacco, Firearms and Explosives.

The operation, not authorized under Justice Department rules, gave agents an off-the-books way to finance undercover investigations and pay informants without the usual cumbersome paperwork and close oversight, according to court records and people close to the operation.

The secret account is at the heart of a federal racketeering lawsuit brought by a collective of tobacco farmers who say they were swindled out of $24 million. A pair of A.T.F. informants received at least $1 million each from that sum, records show.

The scheme relied on phony shipments of snack food disguised as tobacco. The agents were experts: Their job was to catch cigarette smugglers, so they knew exactly how it was done.

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Government records and interviews with people involved reveal an operation that existed on a murky frontier — between investigating smuggling and being complicit in it. After The New York Times began asking about the operation last summer, the Justice Department disclosed it to the department’s inspector general’s office, which is investigating. The inspector general “expressed serious concerns,” court records show.

It is unclear how broadly the A.T.F. adopted this practice, at what level it was approved, and whether it continues. Nearly all references to the A.T.F. have been blacked out of public court records, and most documents are entirely sealed.

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