Al Jazeera's Sebastian Walker, reporting from the Haitian capital Port-au-Prince, said that Jean "is having trouble making it clear that he had been a resident of Haiti for the last five years".
Prior to announcing his intention to run for president, Jean acted as a goodwill ambassador for Haiti, the country where he was born.
The New York-based singer said his role, working for the Haitian government, made international travel and foreign residency necessary parts of his public service.
Jacques Edouard Alexis, a former two-time prime minister and another presidential hopeful, and Leslie Voltaire, a US-educated urban planner and former minister, have also faced scrutiny from the electorial commission.
Some candidates who could be deemed uneligible, including Jean, "have significant support from the streets" and disallowing them to run "could lead to unrest," Al Jazeera's Walker said.
Jean, who left Haiti for the US at age nine, is popular with many Haitians, especially the youth, who see him a national success who never forgot his roots.
Several Haitian youth organisations and Creole music groups have undertaken to support his national campaign as a candidate for the Viv Ansan-m party.
The hip-hop star and three-time Grammy award-winner has, however, been criticised for lacking political experience.
"We await the CEP decision but the laws of the Haitian Constitution must be respected," he said in an email to The Associated Press news agency.
He also told the AP that he had gone into hiding after receiving death threats. Jean said he received a phone call telling him to get out of Haiti and that he was now in a secret location in the Caribbean country.
Preval, the current president, has been widely criticised in Haiti over his handling of the January 12 earth-quake that killed more than 200,000 people and destroyed much of the country's already weak infrastructure.