Hot Fuzz star Pegg, 52, had spoken about his Mission: Impossible co-star in an interview with The Times published on Saturday, but found the jokey story he told about Cruise did not land well with everyone.
Speaking in an Instagram live video after the interview blew up, Pegg said: "I’m currently trending on Twitter for something I said in the Times interview about Tom Cruise never accepting responsibility for his mistakes… like it isn’t just a f****** running joke that we have. Stop being so f****** literal."
He had spoken to The Times about working with Cruise, 59, and said that the Hollywood star managed to maintain authority on film sets by never admitting any wrongdoing.
Pegg had said: "If something goes wrong and it's his fault, he'll flatly deny it. And then if someone corrects him, instead of saying sorry, he'll just say, 'Yeah,' and wink at me.
"I admitted f****** up once and he said - with a wry smile, I hasten to add - 'Simon, don't do that.' He maintains his authority by never being to blame for anything."
Elsewhere in the interview, Pegg had opened up on his alcoholism and shared how he had given up drinking after a spell in rehab - but admitted that he thought he would be dead by now if he was still drinking.
Asked whether he thought the addiction could have killed him, he said: "100%, because, and I don't think it's too dramatic to say, that is the ultimate end of that line of flight."
Pegg had talked about being addicted to the numb feeling that alcohol gave him and how he had come to rely on it after writing about his tough childhood experiences for his 2009 memoir Nerd Do Well.
He had reflected back on his parents' tough divorce and the difficult feeling of not being liked by his stepparents as a child.
Watch: Simon Pegg on how Tom Cruise maintains his superstar authority