Almost one week after the interview was published, the actor decided to sit-down with Charlie Rose where he reiterated his "terrible regret" with the story.
"Let me be clear. My article has failed in that everything that's spoken about is everything but what I was trying to speak about," he explained on Sunday's all-new 60 Minutes.
Charlie added, "But you're really saying, what I really regret is not anything that I did. I regret that people misunderstood what I did."
Penn replied, "That's what I'm saying, yeah."
During his lengthy interview with El Chapo, Sean was able to speak to one of the world's most wanted men about his childhood, experience fleeing from authorities as well as his responsibility in the drug battle.
While El Chapo was ultimately captured days before the article was published, many were quick to criticize the article and Sean's determination to speak with the criminal.
"My article should not have made this much noise," he explained. "El Chapo should not have been this popular a figure to read about."
But when Charlie began to share what many critics were saying—that this was all about Sean's "ego" and that he's an adventurer that "likes being in the center of this"—Sean denied the allegations.
"I absolutely accept that they feel that way," he shared. "No, they're not right."
Sean admitted that he has not heard from anyone in the cartel. Instead, he made it clear that people should be concerned with the state of journalism today.
"I can get angry—like many people can. I'm really sad about the state of journalism in our country," he said. "It has been an incredible hypocrisy and an incredible lesson in just how much they don't know and how disserved we are."
He added, "Again, journalists who want to say that I'm not a journalist. Well, I want to see the license that says that they're a journalist."
60 Minutes airs Sunday nights at 7 p.m. only on CBS.