The Yankees temporarily barred Jackson, a special adviser to the team, after his comments about Yankees Alex Rodriguez and Andy Pettitte and the late New York Mets Hall of Famer Gary Carter, the Post reported.
Jackson did not accompany the Yankees during their weekend trip to Boston.
The Post said he'll resume his advisory role with the team, which includes working with minor leaguers.
Jackson, who threw out the ceremonial first pitch for the Home Run Derby at Kauffman Stadium in Kansas City Monday night, said he had not been banned.
"No, I'm not banned, I'm not suspended," he told the Post. "I still have a great relationship with the Yankees, which I appreciate very much. I've stayed away because of possible disruption being disruptive with the media. It would attract so much attention to it. And I look forward to getting back and doing my job.
"It was a mutual thing it was best because the clubhouse is small [in Boston] and all the media and they didn't want any disruption.''
Jackson was quoted in Sports Illustrated as expressing doubt about Rodriguez's and Pettitte's chances at being inducted to the Hall of Fame because they each admitted to using performance-enhancing drugs.
SI also quoted Jackson as saying Carter and others weren't worthy of being in the Hall of Fame. The comment about Carter caused anger among his former teammates and fans. Carter died in February of brain cancer at age 57.
Jackson said he would apologize to Carter's wife for "inappropriate comments" and said he had spoken with Rodriguez and Pettitte on Friday and has been in contact with Yankees President Randy Levine.