Wally Pfister dismissed the director's summer blockbuster The Avengers as "an appalling film".
"I'm sorry to hear it, I'm a fan," Whedon told Entertainment Weekly.
"What's really important is storytelling. None of it matters if it doesn't support the story," Pfister told the Herald Tribune.
"I thought The Avengers was an appalling film. They'd shoot from some odd angle and I'd think, why is the camera there?
"Oh, I see, because they spent half a million on the set and they have to show it off. It took me completely out of the movie.
"I was driven bonkers by that illogical form of storytelling."
Pfister has served as Christopher Nolan's director of photography since Memento.
Whedon's Avengers sequel is scheduled for release in May 2015.
Watch the trailer for The Avengers below: