Peters claimed that the Ghana midfielder grew tired of racism in Serie A and considered the issue a factor in his move back to the Bundesliga last month.
Schalke have moved to issue a full retraction of those comments, with Peters declaring that he will say sorry to the Boateng in person for the misunderstanding later this week.
A message released on the club's official website read: "A statement made by Schalke finance director Peter Peters regarding the transfer of Kevin-Prince Boateng caused something of a stir on Monday, a misunderstanding that Peters deeply regrets.
"Having spoken to our general manager, Horst Heldt, my initial assumption proved to be completely wrong. He confirmed that racist incidents were definitely not the reason for Kevin's move to Schalke.
"As soon as I'm back at Schalke I will speak to Kevin personally and apologise for what I said. It was certainly not my intention to cast false aspersions on AC Milan or the Italian fans."
Jens Keller's side are back in Bundesliga action this weekend, with Boateng expected to make his second Schalke start against Mainz 05 on Saturday.