The transfer drew protests from some families of the victims, who said it was an "insult" that remains possibly belonging to their loved ones were being put in an underground repository at the site of the 2001 attacks, which killed nearly 3,000 people.
The transfer was carried out in a somber procession of some 15 vehicles that left early today from the New York Medical Examiner's Office on Manhattan's East Side.
The remains were in metallic, rectangular cases.
"They were military transfer cases wrapped with the American flag. They were not coffins," police spokesman Carlos Nievas said.
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Relatives of victims awaited their arrival at the Memorial Museum.
Of the 2,753 people declared missing at the World Trade Center site, 1,115 -- or about 40 percent of the total -- have not been identified, according to the medical examiner's office.
Authorities recovered 21,906 human remains in the area, of which 7,930 could not be matched with the DNA of relatives of the victims.
"We are outraged. There is anger and anguish. It's an insult and a sacrilege," said Sally Regenhard, vice president of a group of relatives of 9/11 victims whose firefighter son was killed in the collapse of the World Trade Center.
"The city has refused to survey the families of the victims to get their opinion because they know the majority is against this plan," she said.
The repository is 65 feet (20 metres) underground and the public will not have access to it. It will remain under the control of the New York Medical Examiner's Office.