The legendary writer questioned why his long-time partner's name would have been credited for the film.
"I don't know how to answer that because in what way would his name appear?" Lee said in response to a question from Moviefone regarding the controversial exclusion.
"Well it's mentioned in every comic book; it says 'By Stan Lee and Jack Kirby'," he continued. "You're talking to the wrong guy because I have nothing to do with the credits on the movies.
"I'm credited as one of the executive producers because that's in my contract. But Jack was not an executive producer. So I don't know what he'd be credited as. Again I know nothing about that, I have nothing to do with the movie's credits."
There has been some backlash against the failure to acknowledge Kirby, with veteran creator Steve Bissette and James Sturm, co-founder of the Centre for Cartoon Studies, both calling for a boycott of the film.
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Lee and Kirby collaborated on the majority of Marvel Comics' most popular characters, including the Fantastic Four, the X-Men, the Hulk, Iron Man and Thor.
Kirby broke away from Marvel in 1970, and maintained a frosty relationship with the publisher and his former collaborator, arguing over the rights to his creations until his death in 1994.
The Avengers will open in UK cinemas tomorrow (April 26) and on May 4 in the US.
Watch a clip from With Great Power: The Stan Lee Story, in which Lee talks about Kirby, below: