The apology came one day after Culliver told a radio host that he would not welcome a gay teammate, particularly in the locker room.
"The derogatory comments I made yesterday were a reflection of thoughts in my head, but they are not how I feel," Culliver said in a statement released by the team. "It has taken me seeing them in print to realize that they are hurtful and ugly. Those discriminating feelings are truly not in my heart. Further, I apologize to those who I have hurt and offended, and I pledge to learn and grow from this experience."
The 49ers said in a statement earlier Wednesday they had addressed Culliver's comments, but didn't elaborate on whether the second-year player would face disciplinary action or a fine.
Culliver made his derogatory remarks during an interview Tuesday with comedian and radio personality Artie Lange, who said he was doing a "goofy interview and asking him all sorts of stupid questions" when he asked the cornerback "whether there is any gay guy on the 49ers."
Culliver, 24, planned to address his remarks formally at 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 told The Associated Press 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 49ers issued a statement before Culliver's apology, condemning his comments one day after Lange played the audio recording of his interview with the cornerback during his radio show.
"The San Francisco 49ers reject the comments that were made yesterday, and have addressed the matter with Chris," the team's statement said. "There is no place for discrimination within our organization at any level. We have and always will proudly support the LGBT (lesbian, gay, bisexual and transgender) community."
Culliver is San Francisco's primary nickel cornerback and had a key interception against the Atlanta Falcons in the NFC Championship Game. The second-year veteran made it clear to Lange that he would not accept a gay teammate.
"I don't do the gay guys. I don't do that," Culliver told Lange, who had asked the cornerback if he ever had been approached by a homosexual player.
Culliver's remarks came one day after a pretrial hearing for former 49ers offensive lineman Kwame Harris, who was charged with felony domestic violence and assault charges from an August beating involving a former boyfriend.
Culliver indicated that a gay player would not be welcome on the 49ers when Lange asked if there were any gay players on the team.
"We ain't got no gay people on the team," Culliver told Lange. "They gotta get up out here if they do. Can't be with that sweet stuff. ... Nah, can't be ... in the locker room, man."
When asked by Lange if a gay player should keep his sexual orientation a secret, Culliver stated that gay players should reveal their sexuality after retiring.
"Gotta come out 10 years after that," Culliver said.
Several NFL teams recently have become concerned about the NFL's credentialing process for the Super Bowl media interview sessions mandatory for all players and coaches on the competing teams.
There is a sense the league should create a more responsible process that scrutinizes media applications and to avoid exposing players to media representatives who might never be approved for credentials to NFL games.
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.
Although a handful of former NFL players have come out as gay, none has while still wearing a uniform.
Harris' defense lawyer, Alin Cintean, said his client identifies as gay but "is not very public about it." Harris, 30, was San Francisco's first-round draft pick in 2003 and spent five seasons with the Niners. He played with the Oakland Raiders in 2008 but was released after the season, his last in the NFL.
Information from The Associated Press was used in this report.