The filmmaker wasn't always a fan of the format, but told comicbookmovie.com he is now having fun playing around with it.
He said: "3D was something that, frankly, I was not a big fan of to begin with. 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."
JJ - who has enlisted Chris Pine, Zachary Quinto and Benedict Cumberbatch to star in the sci-fi film - 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."
Star Trek Into Darkness is set to open next May.