In a Huffington Post blog, Charles Ferguson said pressure from Clinton supporters in the Democratic Party led to many sources shying away.
In August, the opposing Republican Party voted to boycott debates on CNN if the programme went ahead.
It also said it would boycott NBC, which plans a mini-series on Clinton.
The latter series, still in the early stages of production, is set to star actress Diane Lane as the former First Lady.
Mrs Clinton, wife of President Bill Clinton, has been closely watched as a possible contender for the Democratic Party’s 2016 nomination since leaving her position as secretary of state under President Barack Obama in January.
In his blog, Ferguson wrote: “When I approached people for interviews, I discovered that nobody, and I mean nobody, was interested in helping me make this film.
“Not Democrats, not Republicans – and certainly nobody who works with the Clintons, wants access to the Clintons, or dreams of a position in a Hillary Clinton administration.
“After painful reflection, I decided that I couldn’t make a film of which I would be proud. And so I’m cancelling. (Not because of any pressure from CNN – quite the contrary).
“It’s a victory for the Clintons, and for the money machines that both political parties have now become. But I don’t think that it’s a victory for the media, or for the American people.”
The Republican National Committee (RNC) had claimed both the CNN and NBC productions amounted “to little more than extended commercials promoting former Secretary Clinton” and “political ads masked as unbiased entertainment”.
CNN has not commented on the cancellation of the project.