Penn, who has been heavily involved in the Haitian earthquake relief effort long after other stars have moved on, told CNN's Wolf Blitzer he questions the Haitian-born, New Jersey-raised Jean's motives.
"This is somebody who's going to receive an enormous amount of support from the United States, and I have to say I'm very suspicious of it, simply because he, as an ambassador at large, has been virtually silent," said Penn. "For those of us in Haiti, he has been a non-presence."
Jean, 37, who made it big as a member of The Fugees in the 1990s, announced on "Larry King Live" that he has filed papers to run for president in November, said he hopes to help rebuild his homeland.
"Now that our country has toppled, it's a chance to rebuild from the bottom on up," Jean said, adding he will be the voice of Haiti's youth.
But Penn, who has actually been living in Port-au-Prince for several months, is dubious about Jean's commitment.
"What the Haitian people need now is a leader who is genuinely willing to sacrifice," Penn said. "I haven't seen or heard anything of him in these last six months that I've been in Haiti. I think he's an important voice. I hope he doesn't sacrifice that voice by taking the eye off the very devastating realities on the ground."
Jean, 37, established the Yelé Haiti foundation in 2004, providing aid and opportunities to the country's citizens. But in the aftermath of the devastating earthquake that struck the island nation Jan. 12, killing more than 220,000, he was accused of mishandling $400,000 in relief donations.
"He claims he didn't do it," Penn said. "That has to be looked into it. I've been there. I know what $400,000 could do for these people's lives."