In the piece, published in the July 9-16 issue, Jackson took aim at the Hall of Fame for inducting what he believes to be unworthy players -- a group that he said includes Gary Carter, Kirby Puckett, Phil Niekro, Don Sutton, Jim Rice and Bert Blyleven.
"In trying to convey my feelings about a few issues that I am passionate about, I made the mistake of naming some specific players," Jackson said in the statement.
"This was inappropriate and unfair to those players, some of which are very close friends of mine. I think there are ways to speak from the heart without hurting people, and I'm disappointed that I didn't take greater care in expressing my views."
Jackson also said in the article, written by Phil Taylor, that there are "real questions" about the legitimacy of Alex Rodriguez's home run total. Rodriguez has admitted to using performance-enhancing drugs for three seasons from 2001-03.
Jackson said in the SI piece that he would not attend the Hall of Fame induction ceremonies for any player believed to have used PEDs, with the possible exception of Andy Pettitte, whom he considers a friend.
"With friends like that," Rodriguez quipped, "who needs enemies?"
The 66-year-old Jackson was told to stay away from the Yankees during their trip last weekend to play the Red Sox at Fenway Park, which Jackson explained was a "mutual" decision so as not to be a distraction in a crowded clubhouse. His position of special adviser with the Yankees is not believed to be in jeopardy.
Jackson attended Monday's State Farm Home Run Derby at Kauffman Stadium, throwing out a ceremonial first pitch, and said that he has not been banned or suspended by the Yankees.
"I have been proactively reaching out to make personal apologies to those within the Hall of Fame community that I offended, and to the Yankees organization for any disruption that I caused in the clubhouse," Jackson said in the statement. "I continue to have a strong relationship with the club, and look forward to continuing in my role with the team. As always, I remain dedicated to the great game of baseball."
It is not known when Jackson will return to the Yankees' clubhouse. His role with the club involves being available for the Major League team during Spring Training and the regular season, as well as the Yankees' farm affiliates.