Pastor Sean Harris of Berean Baptist Church made the comments, widely circulated on the Internet, in a sermon Sunday, WXII-TV, Winston-Salem, N.C., reported.
"Dads, the second you see that son dropping the limp wrist, you walk over there and crack that wrist. Man up. Give them a good punch. OK?" Harris said in the sermon.
Harris' comments came a week before North Carolina voters were to consider an amendment to the state's constitution limiting legal unions to marriage between a man and a woman.
In an apology on the church's Web site, CNN reported, Harris wrote: "I did not say anything to intentionally offend anyone in the LGBT community. My intent was to communicate the truth of the Word of God concerning marriage. My words were not scripted. It is unfortunate I was not more careful and deliberate."
In the sermon, Harris also said parents who see boys dressing like girls should be "squashing that like a cockroach."
He said he had received e-mails from more than 300 people upset by his comments.
"I know what it was like for me growing up, knowing I was different and knowing I was gay. I can only [shudder] to imagine how a gay kid sitting in the pews would feel after hearing that," said Stuart Campbell, executive director of Equality NC.
CNN said Harris told the Fayetteville Observer his comments were meant as a joke.
And WXII-TV reported he said: "The people who listen to me preach every Sunday understood that I was not advocating that a father would do such a thing. The context of the sermon, the words that immediately followed with regards to loving homosexuals provided the balance, provided the context to what I was saying.
"But if you remove it, and isolate the quote, then I can clearly understand how someone would be offended. And that's why I issued a statement of apology."