J. David Grissom, the chairman of the board of trustees, said that he had spoken to Schnatter on Wednesday.
"Regardless of the context, I apologize", the statement said.
But this wasn't the first time Schnatter had triggered a public outrage.
John Schnatter, founder and ex-CEO of Papa John's, is apologizing for his words.
On Wednesday, a Forbes report emerged alleging that Schnatter had used the slur during the May marketing call. He also complained the Kentucky Fried Chicken founder never faced the kind of public backlash as Papa John's did. He added that Sanders didn't stir public outcry with his racist remarks.
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There are more than 3,400 Papa John's restaurants in the United States and Canada, including 40 in New Jersey.
On Thursday, some current Louisville football players tweeted that they wanted the Papa John's name off their home stadium.
Schnatter also reportedly discussed his early life in IN, telling those on the conference call that "people used to drag African-Americans from trucks until they died". Pizza Hut replaced Papa John's as the NFL's official pizza sponsor earlier this year.
Schnatter admitted that the accusations were true and apologized for his actions in a separate statement to Forbes yesterday. Laundry Service also broke off its relationship with the company.