Abrams's new Star Trek franchise exists in an alternate reality of the original television series and films, although the appearance by Leonard Nimoy in the 2009 movie ties the universes together.
Burton – who played Geordi La Forge in Star Trek: The Next Generation – has now admitted to ET Online that he has problems with Abrams's series.
"JJ [Abrams] [is] a very good director, he really is," Burton stressed. "He directed the hell out of the first movie. I'm really interested to see what he wants to talk about in his upcoming movie."
The actor continued: "I'm disappointed, quite frankly, that his timeline negates the existence of Next Gen. I think that's silly."
Abrams was also recently criticised by original series star William Shatner for agreeing to direct Star Wars Episode 7 in addition to his work with Star Trek.
"He's probably the most talented director of that ilk that we have, but he's gone too far this time," Shatner said earlier this week.
His Star Trek co-star George Takei previously offered a more favorable reaction to Abrams's work, saying: "I showed the path to JJ. [He] came and thought out of the box [with 2009's Star Trek]."
Star Trek into Darkness opens on May 17 in the UK and the US.
Watch a trailer for the movie below: