Apatow, an avowed Howard Stern Show fan, took to Twitter earlier this week to reveal that he gets bored when Stern discusses his new judging job.
"I hate to say it, but I don't have much interest in discussions about America's Got Talent. I tried. It is just too much synergy," the director recently tweeted.
Stern reacted on his radio programme on Monday (April 16) by urging Apatow to stop listening to his show.
"I don't call him out on every artistic decision he makes… you're not down with it, get the f**k off my channel," Stern declared, adding: "No need to whack me from the side of the head."
The controversial radio host also insulted Apatow's box office disappointment Funny People.
"The worst film ever... The worst movie ever made," he said. "Talk about going on and on. I'll take advice from someone who didn't go on and on in their movie."
Stern went on to mock Apatow's penchant for casting his wife Leslie Mann in his films.
Apatow appeared not to be upset by Stern's on-air tirade when quizzed by his Twitter followers.
"All Of Our work is debated. That is part of it. I don't get a free pass either does he. My comment was not even interesting, (sic)" he wrote.
"It gets blown out of proportion by the press who has nothing to write about and Howard who has time to fill. We all Like Certain parts… I like em all. Just some more than others."
Apatow has appeared as a guest on The Howard Stern Show in the past, including in 2009 to promote Funny People with Seth Rogen.
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Watch Howard Stern respond to Judd Apatow's criticism below: