The New York Post said Whitaker, in town to film "Black Nativity," was about to leave the Milano Market on Broadway when one of the workers allegedly saw him take an item from a shelf.
The worker allegedly stopped Whitaker and gave him a patdown in the store, The Post said.
No stolen items were found.
Whitaker's driver, Reggie Crupe, said he saw an employee come out of the store and apologize to Whitaker.
"He told Mr. Whitaker that the cameras in the store were at a bad angle and that he could not see if Forest had stolen anything," Crupe said.
The Post said the employee offered Whitaker free food as part of his apology.
Whitaker's spokesman said the incident violated the actor's rights and upset him.
The Post said the store employees have denied the incident occurred.