The Boston Globe said Darryl McCauley has been charged with larceny, forgery and larceny by continuous scheme, following his arrest at his Wilmington, Mass., home Tuesday.
The arrest reportedly stemmed from a complaint Cook and his lawyer filed with Attorney General Martha Coakley's office and the office's subsequent investigation into the matter.
McCauley, who worked as the comedian's business manager from the early 1990s until earlier this month, is accused of transferring millions from his former client's business accounts to his own personal accounts between July 2007 and December 2008, the newspaper said.
E! News said McCauley pleaded not guilty Wednesday to all of the charges against him. He is being held on $3 million bail.
Cook, a stand-up comedian, has appeared in the films "Mystery Men," "Good Luck Chuck," "Dan in Real Life," "Employee of the Month" and "My Best Friend's Girl."