The Clintons allegedly demanded more control over the interview questions and the final cut. Coming from the Oscar-winning director, the project was filmed during the last two years as the former president was making philanthropic trips to Africa and other places, reported New York Times.
It was backed by HBO which produced films about Ronald Reagan and George H W Bush in the past.
The Clintons didn't want to risk any possible unflattering camera angle that could provide ammo against Hilary's campaign.
"It's not happening soon but that doesn't mean it's not going to happen," a representative for HBO said of the documentary.
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Meanwhile, Matt McKenna, a spokesman for Bill Clinton, branded the rumoured control issues "inaccurate." Chelsea's camp also dismissed report that she sought to join the production.
Scorsese hasn't commented on the matter, but he once said in 2012 that the movie would "provide greater insight into this transcendent figure."
Bill Clinton himself at the time said he was pleased to become the subject of a "legendary director.