The 79-year-old actor and LGBT activist, in a lengthy Facebook post, said his comments were taken out-of-context.
The actor, who played Hikaru Sulu in the original 1960s TV show and the subsequent movies that featured the original cast, said he is "not disappointed that there is a gay character in Star Trek".
"On the contrary, as I made clear, I am delighted that the Star Trek franchise has addressed this issue, which is truly one of diversity. It is thrilling to know that future generations will not see LGBTs go wholly unrepresented in the Trek universe," he said.
"While I understand that we are in an alternate timeline with the new Trek movies, for me it seemed less than necessary to tinker with an existing character in order to fulfill Gene's hope of a truly diverse Trek universe.
"And while I am flattered that the character of Sulu apparently was selected as an homage to me, this was never about me or what I wanted. It was about being true to Gene's vision and storytelling."
"So the lack of gay characters was not some oversight by him; it was a conscious decision with which he grappled."
Takei ended his post by wishing actor John Cho, who is the new Sulu in the movie franchise. He also congratulated Simon Pegg on his daring and groundbreaking storytelling.
"While I would have gone with the development of a new character in this instance, I do fully understand and appreciate what they are doing-as ever, boldly going where no one has gone before," he said.
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