"It is inappropriate for him to be representing us given the disparity between his views and ours," Stern said in a statement Thursday.
Hardaway apologized for his comments, which came a week after John Amaechi became the first former NBA player to say he was gay.
"As an African-American, I know all too well the negative thoughts and feelings hatred and bigotry cause," Hardaway said Thursday in a statement issued by his agent. "I regret and apologize for the statements that I made that have certainly caused the same kinds of feelings and reactions.
"I especially apologize to my fans, friends and family in Miami and Chicago. I am committed to examining my feelings and will recognize, appreciate and respect the differences among people in our society," he said. "I regret any embarrassment I have caused the league on the eve of one of their greatest annual events."
Hardaway represented the NBA in Las Vegas this week at a Habitat for Humanity event and a fitness promotion. The former U.S. Olympian was originally scheduled to be an assistant coach at a wheelchair game Thursday night and later appear at the fan-oriented Jam Session.
"I don't need Tim's comments to realize there's a problem," Amaechi told The Associated Press in a phone interview earlier in the day. "People said that I should just shut up and go away _ now they have to rethink that."
On a Miami radio show Wednesday, Hardaway was asked how he would interact with a gay teammate.
"First of all, I wouldn't want him on my team," the former Miami Heat star said. "And second of all, if he was on my team, I would, you know, really distance myself from him because, uh, I don't think that is right. I don't think he should be in the locker room while we are in the locker room."
When show host Dan Le Batard told Hardaway those comments were "flatly homophobic" and "bigotry," the player continued.
"You know, I hate gay people, so I let it be known. I don't like gay people and I don't like to be around gay people," he said. "I'm homophobic. I don't like it. It shouldn't be in the world or in the United States."
Hardaway also said if he did find out that a teammate was gay, he would ask for the player to be removed from the team.
"Something has to give," Hardaway said. "If you have 12 other ballplayers in your locker room that's upset and can't concentrate and always worried about him in the locker room or on the court or whatever, it's going to be hard for your teammates to win and accept him as a teammate."
Later that night, Hardaway apologized during a telephone interview with WSVN-TV in Miami.
"Yes, I regret it. I'm sorry. I shouldn't have said I hate gay people or anything like that," he said. "That was my mistake."
Two major gay and lesbian groups denounced Hardaway's remarks.
"Hardaway's comments are vile, repulsive, and indicative of the climate of ignorance, hostility and prejudice that continues to pervade sports culture," said Neil Giuliano, president of the Gay & Lesbian Alliance Against Defamation. "And by apologizing not for his bigotry, but rather for giving voice to it, he's reminding us that this ugly display is only the tip of a very large iceberg."
Said Matt Foreman, president of the National Gay & Lesbian Task Force: "Hardaway is a hero to thousands of young people. And that's what makes his comments so troubling. Sadly, his words simply put the pervasive homophobia in the NBA on the table."
Amaechi, who detailed his life in his recent autobiography "Man in the Middle," oped his coming out would be a catalyst for intelligent discourse.
"His words pollute the atmosphere," Amaechi said. "It creates an atmosphere that allows young gays and lesbians to be harassed in school, creates an atmosphere where in 33 states you can lose your job, and where anti-gay and lesbian issues are used for political gain. It's an atmosphere that hurts all of us, not just gay people."
Amaechi taped a spot Thursday for PBS' gay and lesbian program "In the Life." He said the anti-gay sentiment remains despite Hardaway's apology.
"It's vitriolic, and may be exactly what he feels," he said. "Whether he's honest or not doesn't inoculate us from his words. It's not progress to hear hateful words."