CEO John Schnatter complained about NFL players' national anthem demonstrations on an earnings call earlier this month, and seemed to blame a decline in Papa John's sales on the fallout from those protests. "That definitely was not our intention".
CEO and TV pitchman John Schnatter previously said the National Football League anthem protests have hurt his pizza sales.
"This should have been nipped in the bud a year and a half ago", Schnatter said.
The pizza chain said that it supports "the players' movement to create a new platform for change" but that it also believes that "as Americans, we should honor our anthem".
In response to a Twitter user's wry observation that Papa John's "really needed 2 weeks to come up with a "sorry you were offended" statement", the company replied, "We agree it took too long".
"We will work with the players and league to find a positive way forward", Papa John's continued.
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The chain then used an emoji for the middle finger, "those guys".
"Leadership starts at the top, and this is an example of poor leadership", he added, apparently calling out commissioner Roger Goodell.
In a series of tweets on Tuesday, the company apologized to anyone who found the comments "divisive". Open to ideas from all. It got worse for Schnatter when the far-right website The Daily Stormer declared Papa John's to be "the official pizza" of the alt-right.
Several prominent figures criticized Schnatter for his initial insensitive comments, insinuating that pizza sales are more important than taking a stand against racism and police brutality - the reasons behind the majority of players protesting during the anthem.