Officials of the Nation of Islam were first invited to Jackson's Neverland Ranch several weeks ago to provide security.
But increasingly they have exerted control over the pop star's schedule, media relations and business affairs, the newspaper reported.
Jackson faces charges of child molesting in Santa Barbara and recently moved into a rented house in Los Angeles, where about half a dozen Nation of Islam officials routinely accompany him.
Efforts to reach Jackson through his spokesman were not successful, but his lawyer, Mark Geragos, and The Final Call, the Nation of Islam's newspaper, denied the claim.
On Monday, Jackson's official spokesman, Stuart Backerman, resigned to protest the Nation of Islam's presence, according to one of Backerman's colleagues.

