Joe Berlinger, the Oscar-nominated director who helped free the West Memphis Three with his “Paradise Lost” documentaries, returns to world of courts and crime in his latest film, “Whitey: United States of America v. James J. Bulger.”

This time his subject is legendary fugitive Whitey Bulger, the former Winter Hill Gang chief whose flight from justice has inspired a cottage industry of films and books, and who almost no one believes was wrongly accused of being a brutal thug.

Berlinger’s film, which opens on June 27, may not be interested in exonerating Bulger, but it has generated a wave of attention and headlines by giving weight to the gangster’s denials that he was an FBI informant.

“There are some compelling arguments that the informant story was a cover story for a deeper story about corruption at the FBI,” said Berlinger.

“This is not an apology for James ‘Whitey’ Bulger,” he adds. “He’s a killer, who deserves to be behind bars.”

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Questioning the Boston crook’s reputation for being the ultimate rat has led to blowback from Bulger chroniclers such as the Boston Globe’s Kevin Cullen and “Black Mass” co-author Dick Lehr.

“The film quite intentionally, quite cynically, and quite inaccurately suggests that Whitey’s unsubstantiated claim that he wasn’t an informant is legitimate,” Cullen wrote in a recent editorial, that, to be fair, also offers praise for the picture.

Berlinger claims that his critics have skin in the game.

“People are accusing me of intellectual dishonesty, but is there anything more intellectually dishonest than people with a vested interest in a story that they’ve made money off of challenging another point of view?” he said.

It’s a portrait of Bulger that stands to get more fixed in the public’s mind with the release next year of a film version of “Black Mass,” starring Johnny Depp as the gangster.

“I love Johnny Depp and I wish him well playing Bulger and I think it’s brilliant casting, but that movie is based on a potentially flawed story,” Berlinger said.

Berlinger’s film argues that Bulger’s defense team was unfairly barred from raising issues about whether or not their client was an informant, and were denied a chance to offer up a counter-narrative that he was allowed to operate with impunity because of more systemic corruption within the FBI. The director maintains that it may be in the bureau’s best interest to blame the Boston office’s oversight on a few bad apples — namely Special Agent John Connolly, Bulger’s alleged handler, who is currently serving a 40-year prison sentence — rather than risk overturning past convictions and exposing the office to legal liability.

Yet, Berlinger acknowledges that he is not convinced Bulger is telling the truth when he claims he was buying information from his FBI contacts instead of trading it, or that he was innocent of the murders of two women, Debra Davis and Deborah Hussey.

“The film presents lots of questions without providing a lot of answers,” Berlinger said. “It’s possible that in order to pass into metaphorical criminals’ hall of fame, he needs for people to think he’s not rat and he’s not a killer of women.”

In addition to presenting alternative views on Bulger’s criminal legacy, the film offers the novel experience of hearing the man himself. It meant convincing the gangster’s attorneys — who said they had turned down interview requests from the likes of Barbara Walters — that he would treat their client fairly.

“Here was somebody who was seemingly very objective,” said Hank Brennan, Bulger’s defense attorney. “I looked at his past films and it was clear to me that Joe Berlinger wasn’t afraid to confront the government or portray a story in way that may embarrass people.”

Though Berlinger’s attempts to interview Bulger in person were barred by the government, he was able to film a telephone conference between the gangster and his defense team.

“Getting Bulger on tape was, I think, a major coup in the film, because even though there’s dozens of books and many screenplays written about him, Bulger has never spoken for himself,” Berlinger said. “Whether you buy what he’s saying or not, is a question I want the audience to ask themselves.”