The Defense Department’s internal watchdog upheld the complaints of a National Security Agency official early in the George W. Bush administration who said the agency was misspending millions of dollars on a technically flawed system for sifting through digital communications, according to conclusions released for the first time Wednesday.

NSA official Thomas A. Drake, whom the government unsuccessfully tried to prosecute for violations of the Espionage Act, and others at the agency prompted the highly classified study by making a call to the Pentagon inspector general’s fraud, waste and abuse hotline.

While the November 2004 report evidently did not support any allegations of criminal wrongdoing by top NSA officials, its conclusions make clear that the so-called Trailblazer program had problems and that a rival system Drake favored stood a reasonable chance of success.

“The National Security Agency is inefficiently using resources,” the report stated, and “may be developing a less capable long-term digital network exploitation solution that will take longer and cost significantly more to develop.”

A private watchdog group, the nonprofit Project on Government Oversight, released a heavily redacted copy of the report after obtaining it under the Freedom of Information Act.

Drake — who persistently described himself as a whistleblower who never leaked official secrets — was the target of an espionage prosecution from 2007 until last week, when the Justice Department dropped the most serious charges against him and accepted his plea of guilty to unauthorized use of a government computer used to communicate with a reporter. His sentencing is slated for July 15.

The Pentagon report suggested that the NSA had “disregarded solutions to urgent national security needs” and said it had evidence that the agency “modified or suppressed” pertinent studies. It also said that some sources of criticism feared reprisal.

Top NSA officials rejected the early criticism of Trailblazer, with its deputy chief of staff telling the inspector general’s office that the agency “nonconcurred” with its key conclusions. But the cost and technical problems that surfaced in two independent scientific reviews disclosed in the report eventually forced the NSA to abandon the program in 2006, after it had consumed more than $1 billion.

“This is just more evidence that the government never should have prosecuted Thomas Drake,” said Danielle Brian, executive director of the Project on Government Oversight. “We should be thankful that Mr. Drake had the courage to stand by his convictions and do what was best for the country.”