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Mr. Black returned to work at SAIC after his retirement from the NSA in 2006.

Through a spokesman, SAIC said the company and its executives declined to comment.

Mr. Drake, who held a senior position at NSA from 2001 until 2008, said the agency had planned to spend more than $4 billion on the program with SAIC and dozens of other contractors, and that fraud and abuse were widespread in Trailblazer and related programs.

“It really became a feeding frenzy as contractor after contractor bellied up to the Trailblazer bar,” he said.

Mr. Drake said NSA’s accounts — like most other Defense Department bookkeeping systems — were “unauditable.”

The agency’s budget is classified, but even for those inside the agency, “It was very difficult to determine where most of the money was going except at a very general level,” he said.

The government “fought very hard” to keep any reference to the inspector general’s report, or his other whistleblowing activities, for instance to Congress, out of the court case.

“Why were they so afraid of that getting into court?” he asked. “It’s the continuing cover-up.”

The NSA press office referred a request for comment to the Justice Department.

Ms. Sweeney, the Justice spokeswoman, said: “The department has long valued the legitimate exposure of waste, fraud and abuse if it occurs while at the same time protecting the rule of law.

“There are laws prohibiting government employees who are entrusted with the nation’s most sensitive information from disclosing classified information to anyone not authorized to receive it.”

Despite the administration’s pursuit of leaks, some observers say, such cases often are difficult to prosecute without exposing secrets that the government wants to protect.

A former U.S. official familiar with the Drake case called leak cases challenging.

“You have to make absolutely sure that the victim agency understands very clearly who will be called as a witness and what they might be asked about,” the former official said. “They have to be OK with that. … If that is not adequately or sufficiently discussed, problems can come up.”