The studio commissioned the project following the director's success with Coraline, but the movie is now seeking a new home.
Selick, best known for directing The Nightmare Before Christmas, previously helmed the Disney-distributed James and the Giant Peach.
He is also collaborating with Coraline writer Neil Gaiman to bring one of the authors' other works, The Graveyard Book, to the big screen. It is not yet known whether the project will be a live-action or animated venture.
Variety reports that Selick's mystery movie has been in development since last summer, but specific details about the film have not been disclosed.
Disney is also on board for the The Graveyard Book adaptation, which is said to have not been affected by the cancellation of Selick's other undertaking.
Watch a trailer for Coraline below: