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 / Updated  / Source: NBC News
By Tracy Connor and Tom Winter

A former Boston FBI official has been indicte on charges he lied on the witness stand during Whitey Bulger's trial to help the ruthless mobster.

Bob Fitzpatrick, who was demoted and resigned from the agency in 1986, pleaded not guilty Thursday afternoon to 11 counts of obstruction of justice and perjury.

"From approximately 1998 through the present, the defendant Fitzpatrick has falsely held himself out as a whistleblower who tried to end the FBI's relationship with Bulger," the indictment says.

The court papers say Fitzpatrick, who supervised the Boston organized crime squad in the 1980s, lied during the trial about his dealings with Bulger as an FBI agent — and falsely claimed under oath that he found the rifle that was used to assassinate Martin Luther King Jr.

Bulger, 84, was convicted in August 2013 of dozens of crimes stemming from his bloody reign over Boston's underworld as the head of the Winter Hill Gang. The gangster, who spent 16 years on the run, is serving life but is appealing.

Fitzpatrick testified for the defense and sources said the charges against him do not imperil Bulger's conviction.

Bulger's lawyer, Hank Brennan, told NBC News that the charges against the retired agent would not affect the appeal but claimed the government was retaliating against Fitzpatrick for defying and "embarrassing" them.

"The government can't be that concerned about perjury. I spent weeks impeaching their witnesses," Brennan said of the admitted murderers who took the stand for the prosecution during the trial.

During his trial testimony, Fitzpatrick told the court that Bulger told him in the 1980s that he was not an informant for the FBI. The indictment alleges that Bulger never made that claim to him.

Bob Fitzpatrick a former Assistant Special Agent in Charge of the Boston FBI office has been arrested and taken into custody on April 30, the U.S. Attorney's office confirms.NECN

One focus of Bulger's defense was the claim that he was never an FBI informant, while the government said he was and had a corrupt relationship with an agent, John Connolly, who later went to prison for it.

Fitzpatrick has said he quit the FBI in disgust over corruption, but the indictment charges that he left after being demoted for falsifying reports related to his investigation of an unrelated shooting.

Fitzpatrick wrote a memoir about his experience with Bulger titled "Betrayal: Whitey Bulger and the FBI Agent Who Fought to Bring Him Down."