The 7,930 fragmentary remains in sealed containers were escorted by fire, police and Port Authority vehicles with flashing lights and no sirens from a Manhattan forensics lab to the repository at the site of the National September 11 Memorial & Museum.
The repository will be under the care of the city's chief medical examiner, whose office will continue trying to match the fragments to the more than 1,000 victims of the attacks that have yet to have had any remains identified.
The repository is sealed off from exhibition areas by a wall and will only be accessible to the medical examiner's staff and family members of the victims, who will be able to visit the space even when the museum is closed, the city has said.
Some family members of those killed in the attacks protested the move, saying it was wrong to store the remains at what is essentially a tourist site, adding that the underground repository could be subject to flooding.
They put black bands over their mouths in a silent protest as the procession rolled past.
"The human remains repository is most certainly a part of the museum," Jim Riches, the chairman of the 9/11 Parents & Families of Firefighters and WTC Victims group, said in a statement.
Other family members have supported the move.