A confidential counterintelligence investigation cleared suspended Pentagon analyst Adam S. Lovinger on allegations of leaking data to the news media, but officials never told his defense team.

The Naval Criminal Investigative Service (NCIS) examined Mr. Lovinger’s use of classified computer networks. In a 2018 report, the NCIS said its review “did not reveal any potential CI [counter intelligence] concerns,” according to a copy obtained by The Washington Times.

Mr. Lovinger’s attorney, Sean Bigley, has now filed a complaint with the Defense Department inspector general. He accuses Pentagon officials who targeted his client of a “serious ethics violation” by withholding the exoneration.

The NCIS probe was closed September 2018, and the report signed in November. Mr. Lovinger’s administrative trial began the next month.

Mr. Bigley is trying to convince the Pentagon IG that his client is a victim of whistleblower reprisal. Mr. Lovinger’s employer, the Pentagon Office of Net Assessment, accused him of mishandling “sensitive” material, a charge his lawyer said essentially is made up since there is no such classification.

“This single NCIS document undercuts about 80% of the government’s sham case against him,” Mr. Bigley told The Times. “No wonder DoD withheld it. No leak, and he didn’t have any ‘sensitive’ documents on his computer so he couldn’t have been mishandling ‘sensitive’ information on his computer.”

The NCIS report said an analysis of the hard drive on Mr. Lovinger’s U.S. government-issued Dell computer “did not yield any classified or sensitive information.”

In the declassified version of the report, the word “not” is missing. An NCIS spokesman told The Times on Wednesday that the file copy is being corrected to add the word “not.”

The Lovinger case became a cause celebre for conservatives who believe the Pentagon retaliated against the 12-year employee. He supported President Trump’s policies and went to work for the new White House in 2017. The Office of Net Assessment quickly pulled him back to the Pentagon, where he was suspended and stripped of his security clearance. His pay stopped in April 2018.

Mr. Lovinger lost his appeal in a decision this spring following a five-day closed hearing in December before an administrative judge who ruled in favor of the Office of Net Assessment. One of the overriding narratives during Mr. Lovinger’s battle to keep his job was that he had violated rules by leaking derogatory stories about the office to the news media.

Unknown to him at the time, the NCIS already had conducted an intrusive investigation into his computers and other devices. Agents found no evidence he leaked to the press, as charged, or that he was a counterintelligence risk. It closed the case nearly a year ago. Agents saw no need to interview him because of a lack of evidence of wrongdoing.

Here is the NCIS bottom line in September 2018: “As this investigation has not disclosed indicators Lovinger leaked sensitive information to members of the media and all logical investigative steps were completed, this case is now closed.”

‘Whistleblower reprisal’

Mr. Bigley’s reprisal argument is based on the following chronology:

Before his suspension, Mr. Lovinger complained internally that the Office of Net Assessment (ONA) was not doing its job by failing to produce reports on future threats known as “net assessments.” Instead, the office was awarding contracts for outside academic-style reports, he said.

One paid contractor was Stefan Halper, the Washington national security figure who while at Cambridge University became an FBI informant to spy on Trump campaign associates in 2016.

Here is how Mr. Bigley discovered the NCIS verdict:

Judicial Watch, a conservative investigative nonprofit run by Tom Fitton, joined the Lovinger team. It filed a lawsuit in U.S. District Court to obtain the Pentagon’s file on Mr. Lovinger.

Mr. Fitton hit pay dirt. The Pentagon turned over a number of email threads. Buried in them was a passing reference to the NCIS. Nothing more.

Mr. Bigley then filed an open records request. Last month, the NCIS turned over its 2018 report.

The attorney said he was stunned. He never knew the probe even existed, but less its findings.

He also discovered the Pentagon knew his client was exonerated on the leak issue.

The NCIS report states that the investigative agency specifically informed the Office of Net Assessment.

“ONA was apprised of the status of the investigation,” the report states.

The report also shows that the requesting agency in August 2017 was the Pentagon’s Washington Headquarters Services. It is the organization that revoked Mr. Lovinger’s clearance and brought the case against him.

Mr. Bigley said that NCIS surely informed Washington Headquarters Services of its findings since it had asked for the probe.

The Washington Times submitted a query about Mr. Bigley’s complaint to the Pentagon press office, which didn’t respond.

Mr. Bigley said the administrative judge did not find Mr. Lovinger guilty of leaking to the press. But he said that is beside the point. The attorney said he spent hours preparing a defense on that charge, not knowing there was an NCIS report that already had cleared his client. Government attorneys pressed the leak case during the hearing, he said.

By not being told of the exoneration, Mr. Bigley also was denied the opportunity to present the NCIS report as evidence.

“The leaking allegation against Mr. Lovinger was by far the most serious claim brought against him by DoD,” Mr. Bigley told The Times. “We believe that the government hid this exculpatory evidence because they knew that their other allegations were a smorgasbord of nonsense that would never independently have gotten off the runway.”

In a May 2017 memo, Washington Headquarters Services outlined why it was suspending Mr. Lovinger’s security clearance.

There were two general categories: He mishandled a classified document and shared “sensitive” material with others.

Second, he played a role with a contractor in leaks to the Washington Free Beacon about the Office of Net Assessment’s supposed failings under Director James Baker.

The NCIS report refuted that: “An interview of former ONA contractor did not yield any information of concern.”

“According to Mr. Baker, the leak had disastrous consequences for the ONA mission,” the report added.

In his July letter to the Defense Department inspector general, Mr. Bigley said Pentagon lawyers “failed to make any mention of the NCIS findings in their case, failed to turn over the NCIS investigative report, and failed to even alert this attorney that a report existed which effectively exonerated Mr. Lovinger of the most serious allegation against him.”

That same month, the Office of the Under Secretary of Defense sent Mr. Lovinger a firing memo. Since he needed a security clearance to work at ONA and his had been revoked, Mr. Lovinger was being terminated.

Mr. Bigley fired off a return letter saying the termination was premature.

“Nothing underscores ‘whistleblower reprisal’ quite like rushing to terminate a whistleblower from federal service before the Department’s own IG can complete its statutory obligation of an independent, thorough investigation,” he said.

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