The director admitted during a recent press conference that he was strong-armed into the move by Paramount, but had since grown to appreciate the results.
"3D was something that, frankly, I was not a big fan of to begin with," Abrams said. "Essentially in order for us to make this movie, the studio said 'You gotta do this in 3D'. So we said, well, we can do a 2D version that we love that can also be converted to 3D."
"And the truth is that I've actually been having a lot of fun with it."
He went on to suggest that Star Trek Into Darkness's conversion will be groundbreaking, marking the first time a film has been shot extensively in IMAX before being converted into 3D.
Abrams added: "We have an amazing amount of creative freedom, doing the 3D in post[-production]. This is kind of the myth, that it only looks good if you shoot the movie in 3D, which is completely not true.
"In fact, we're doing a bunch of things with the 3D in this movie that have not been done before, using techniques that have not been seen. All the exterior shots, including the shots in space, are all either shot or rendered in IMAX format.
"It's the first time a movie has been shot in IMAX to this scale and converted to 3D."
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Star Trek Into Darkness will be released on May 14, 2013.
Watch the first trailer below: