The team didn't elaborate on whether the second-year player would face disciplinary action or a fine.
During an interview Tuesday at the Superdome, Culliver responded to questions from comedian Artie Lange by saying he wouldn't welcome a gay player in the locker room. He also said the 49ers didn't have any homosexual players and, if they did, those players should leave.
"The San Francisco 49ers reject the comments that were made yesterday, and have addressed the matter with Chris," the team said. "There is no place for discrimination within our organization at any level. We have and always will proudly support the LGBT community."
Culliver planned to formally address his remarks during a news conference during the 49ers' media availability Thursday morning, according to his personal public relations representative, Theodore Palmer.
"Chris is very apologetic for any harm caused to anyone," Palmer said in a phone interview. "His intent was not that at all. He is one who celebrates the differences of others. All of this was just a big mistake. It was interpreted wrong."
The interview Tuesday began with Lange asking Culliver about his sexual plans with women during Super Bowl week. Lange followed up with a question about whether Culliver would consider pursuing a gay man.
"I don't do the gay guys, man. I don't do that," Culliver said during the 1-minute taped interview. "Ain't got no gay people on the team. They gotta get up outta here if they do. Can't be with that sweet stuff."
Lange asked Culliver to reiterate his thoughts, to which the player said, "It's true." He added he wouldn't welcome a gay teammate — no matter how talented.
"Nah. Can't be ... in the locker room, nah," he said. "You've gotta come out 10 years later after that."
The 24-year-old Culliver, a third-round draft pick in 2011 out of South Carolina, made 47 tackles with two interceptions and a forced fumble this season while starting six games for the NFC champion Niners (13-4-1).
He had his first career postseason interception in San Francisco's 28-24 win at Atlanta for the NFC title.
The 49ers participate in the NFL's "It Gets Better" anti-bullying campaign. The city of San Francisco and progressive, open-minded Bay Area are home to a large gay community.
Messages left for a 49ers spokesman weren't immediately returned.
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