The comedian was revealed to have made a number of anti-gay comments while performing live in Nashville, TN on Friday after a fan who attended the show posted an essay about the incident via his Facebook page.
The 30 Rock star has since clarified his comments, insisting that he is an "equal opportunity jokester" and meant no offence to gays and lesbians.
Morgan said in a statement: "While I am an equal opportunity jokester, and my friends know what is in my heart, even in a comedy club this clearly went too far and was not funny in any context.
"I want to apologise to my fans and the gay and lesbian community for my choice of words at my recent stand-up act in Nashville. I'm not a hateful person and don't condone any kind of violence against others."
Morgan was reported to have told crowds at the Ryman Auditorium that he would "pull out a knife and stab" his son if the child was gay. He also criticised kids who experience bullying as a result of their sexuality, claiming that the victims should "just bust some ass and beat those other little f**kers that bully them, not whine about it".
He was said to have made similar comments during a 2009 show at New York's Carnegie Hall.