Blatter said he was sorry if he offended anyone with his remarks.
"It was not my intention and never will be my intention to go into any discrimination," Blatter said in Abu Dhabi, which is hosting the Club World Cup. "This is exactly what we are against. If somebody feels that they have been hurt, then I regret (it) and present apologies."
Qatar has strict laws against homosexuality. After beating the United States, among other competitors, for the event, the Gulf nation has come under intense scrutiny for its social restrictions, limitation of drinking alcohol, frowning on public affection and considering homosexuality taboo.
Blatter's comments drew immediate ire from gay advocacy groups. Juris Lavrikovs, communications director for the European branch of the International Lesbian, Gay, Bisexual, Trans and Intersex Association, said the comments were "very unfortunate and have left people deeply offended" and said "we are talking about a very basic human right that is being violated."
Lavrikovs said that Qatar and more than 70 other countries still criminalize individuals for homosexual relationships, and some countries even punish them by death sentence.
Herman Ouseley, chairman of Kick It Out, a British campaign group for equality and inclusion in soccer, said earlier this week that he expected better from someone in Blatter's position.
Based on reporting by the Associated Press.