Jones, 19, initially made the comments during a video posted on YouTube Monday by a conservative religious group.
He has subsequently backpedaled on the statements about the show on which he has acted for 10 seasons.
"I apologize if my remarks reflect me showing indifference to and disrespect of my colleagues and a lack of appreciation of the extraordinary opportunity of which I have been blessed," the actor said in a statement Tuesday.
"I never intended that," he said. "Without qualification, I am grateful to and have the highest regard and respect for all of the wonderful people on 'Two and Half Men' with whom I have worked and over the past 10 years who have become an extension of my family."
The Hollywood Reporter said Jones' character, Jake, is not scheduled to appear in the next two episodes of "Men," but it has nothing to do with his comments.