National Geographic Channels CEO David Lyle says the film was indeed recut - but to show less footage of the president than an earlier version of the film.
"I think the end titles run longer than Obama's time on screen," Lyle said.
The movie has been accused by conservatives of having a political agenda in part because of its Nov. 4 premiere date and its backing by Obama supporter Harvey Weinstein. On Wednesday, The New York Times reported that a copy of the film provided to the paper showed that it had been recut to strengthen Obama's role.
Lyle said the movie was "well timed for us because we believe the topic is interesting at all times" and called the notion that two minutes of screen time would affect the election laughable.
"People that haven't seen the movie have decided that it's a political event. Believe me, in 85 million homes, a movie from National Geographic is not going to change the outcome of the election in a country of 300 million," Lyle said.
Produced by Weinstein and National Geographic, the 90-minute film depicts the mission that took down bin Laden. It mixes interviews with flashbacks and archival footage that leads the famed SEAL Team Six squad to a fortified compound where a mysterious 6-foot-5-inch bearded figure was believed to be staying.
It's the first original film to come out of the National Geographic Channel, which has about 85 million viewers, and it's slotted to come out a few weeks before "Zero Dark Thirty," another film about the raid by "Hurt Locker" director Kathryn Bigelow.
Freddy Rodriguez, who plays a Navy SEAL in "SEAL Team Six," said there was no political agenda behind the film.
"I think people who are in the opposing party are going to say that, of course. It's bound to happen because it fell on Obama's watch. And there's footage of him in the film, so how could people not have that criticism? It's almost expected," Rodriguez said.
His co-star, Kathleen Robertson doesn't believe the criticism is fair.
"It's impossible to make a film about the killing of Osama bin Laden without the president being a part of that film," Robertson said.