The remains will receive a police and fire department escort when they travel from the medical examiner's office on Saturday.
The move is renewing a more than decade-long debate among relatives about the best resting final place for loved ones killed in the 2001 terror attacks.
Some feel the repository, which is in the same building that houses the National September 11 Memorial Museum, is an inappropriate setting for the 7,930 unidentified remains. Others are pleased.
The museum opens to the public May 21.
The decision to move the remains was first reported by The New York Times.