David Grissom, the chairman of the university board, said he had spoken to Schnatter on Wednesday.
“After speaking with John, I’m confident that his comments, while inappropriate, do not reflect his personal beliefs or values,” Grissom wrote.
Papa John’s stock plunged to a 12-month low after the report was released.
In November, Schnatter drew criticism after a call with investors in which he blamed slow sales at the company, which is an NFL advertiser, on the league’s “poor” leadership over the anthem demonstrations.
“This year, the ratings have gone backwards because of the controversy,” Schnatter said at the time.