The Dutchman had been quoted as saying the Rossoneri boss forced him out of the club but the 37-year-old insists he has been mistranslated
The Botafogo midfielder was quoted as saying that he had left San Siro last summer because of the 46-year-old coach, a claim subsequently strongly denied by the former Cagliari boss.
Seedorf has now moved to end the controversy by explaining that he was misquoted and that he actually enjoyed a good working relationship with Allegri during their time together at Milan.
"My comments were mistranslated and I'm very sorry about this," the former Netherlands international told Sky Sport24.
"I would never have allowed myself to say things like that because my heart remains at Milan. I'm sorry that a controversy has been created out of nothing.
"As long as I was at Milan, I always respected Allegri. I just explained the reasons for my Milan departure. I never had any type of problem with Allegri.
"A press release will come out soon in which I will explain all the real things I said."
Seedorf was reportedly on the verge of replacing Allegri as coach last summer and there is still talk that he could be approached again at the end of the current campaign.
However, the 37-year-old Dutchman stated: "I'm thinking only of Botafogo. Now is not the time to think about it."
Meanwhile, Seedorf had some words of warning for the Italian press, arguing that they need to leave Mario Balotelli in peace to focus on his football.
"You have to leave him alone," he implored. "He can make the difference but he is young.
"I hope that he continues to be decisive both for AC Milan and Italy."