Asked at a Euro 2012 news conference earlier in the day about media reports there were two "secret" gays in the Italy squad, he said: "That's their problem. I hope there isn't one in the national team."
After criticism from gay groups, Cassano issued an apology through Italian state news agency ANSA.
"I am sincerely sorry that my comments have caused controversy and protests among gay groups. Homophobia is not a point of view that I share. I didn't want to offend anyone and I absolutely don't want to put a person's sexual freedom under discussion.
"I only said that it was a problem which was nothing to do with me and I don't let myself express judgements on other people's choices, which should all be respected."
The often outspoken Cassano also caused a stir by hinting he might leave AC Milan.
Milan are in talks about possibly selling Thiago Silva to megarich Paris Saint-Germain and Cassano said his side may struggle to compete at the very top if they cash in on the Brazilian.
"To lose Thiago is hard, hard. It is impossible to replace him. Without Thiago, it is 50 percent of our team. It's a crime to lose Thiago," the 29-year-old told the news conference.
"At the end of the Euros I will see if I remain at Milan or I leave. I don't know."
He indicated he might have to consider a move if Milan bought Manchester City forward and Italy team-mate Mario Balotelli and said his happiest times were at Sampdoria, where he was kicked out in 2010 for verbally abusing the president.
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