The Super 8 filmmaker told MTV that the alien race will have a role in the upcoming sequel in an "adversarial" role.
Photo gallery - Star Trek Into Darkness in pictures:
Star Trek Into Darkness will see Zachary Quinto, Simon Pegg, Chris Pine, Zoe Saldana, John Cho and Anton Yelchin reprise their roles from Abrams's 2009 reboot of the movie series.
Benedict Cumberbatch joins the cast as a villain referred to as John Harrison, while Alice Eve will debut as Starfleet scientist Carol Marcus. Noel Clarke and Peter Weller are among the other new additions to the cast.
Behind-the-scenes footage from the movie was recently released as well as a new motion poster featuring a voiceover from Cumberbatch with a destroyed London as a backdrop.
Star Trek Into Darkness will open in cinemas on May 17.
Watch the announcement trailer for Star Trek Into Darkness below: