James has defended Paterno from a report that said he should have done more to prevent assistant coach Jerry Sandusky from sexually abusing boys. James also said in a radio interview that men showering with young boys was "quite common in America 40 years ago."
The Red Sox said in a statement that James' views do not represent those of the ballclub. It said owner John Henry and general manager Ben Cherington called James and asked him to stop commenting on the Penn State case.
James is a pioneer in baseball statistics whose title is senior adviser of baseball operations.