Alec previously announced that he would not renew his contract with the hit comedy when it expires in 2012.
Stephen told OK that he does not believe his sibling's claim that he is tired of pursuing his acting career.
"It's a bunch of rubbish," said the Usual Suspects star. "I think he'll continue to do it as long as the show goes."
The actor added that he believes his brother was simply trying to secure a more lucrative agreement with NBC.
"I think that there's ways that they're going to motivate him to stay around," he said.
The fifth season of 30 Rock will premiere in September on NBC.