He and Penn agree on something: Rolling Stone reporting about Mexican drug lord Joaquín "El Chapo" Guzmán failed in its mission.
"To over-demonize any human being is not in our best self-interest," he said.
He spoke about the encounter between the actor and the drug dealer to Spanish newspaper El País.
Penn also insisted he had played no role in Guzmán's eventual recapture.
Obama's national security adviser said that the actor did not participate in any effort to arrest the drug lord.
U.S. investigators will also examine Penn's interactions with Guzmán, but it was unclear if prosecutors would try to force the actor to turn over information about the interview.
Who is Kate del Castillo?
She has the kind of connections in movie and film industry to bring a film about "El Chapo" into reality.
A Rolling Stone spokeswoman did not immediately return requests for comment.
They were onto him in October, but aborted because he was with women and children.
Actors Sean Penn and Kate del Castillo interviewed the famed drug dealer.