Culliver made the comments Tuesday in New Orleans, where the 49ers are preparing to take on Baltimore in Sunday's Super Bowl XLVII, the San Francisco Chronicle reported.
When asked by an associate of radio personality Howard Stern if there were any gay players on the 49ers, he answered, "No, we don't got no gay people on the team, they gotta get up out of here if they do ... can't be with that sweet stuff. Nah ... can't be ... in the locker room man."
The team disavowed Culliver's comments Wednesday.
"The San Francisco 49ers reject the comments that were made yesterday, and have addressed the matter with Chris," the statement said.
"There is no place for discrimination within our organization at any level. We have and always will proudly support the LGBT community."
Coach Jim Harbaugh said in November he had "no discrimination in his heart" against gays, adding that if there were any on the 49ers they would be treated the same as anyone else.