The director revealed that the release will feature at least 30 minutes of deleted scenes.
"My first assembly was three hours long," Whedon told Collider.
Whedon went on to say that most of the footage is character-related.
"It's some character stuff but it was more ancillary," he said. "Marvel never wanted to take the texture out of the movie, the little moments between people.
"We wanted, obviously, to streamline it and make it not so long that it became self-indulgent, which at that length it was, and they wanted to focus on The Avengers more than anything else, but the thing I loved was there were so many little moments that I thought, 'They're going to make me squeeze this out', and they never did," Whedon continued.
"Once we had the structure down, they really wanted it to breathe and for these things to be as textured as they could be."
The Avengers opens in US cinemas on May 4, and in the UK as Marvel Avengers Assemble on April 26.
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Watch a trailer for The Avengers below: