Thousands of unidentified remains belonging to victims of the 9/11 attack have been returned to Ground Zero, the World Trade Center site that is now a memorial and museum.

The move has drawn protests from some relatives, who say it’s an “insult” that remains possibly belonging to their loved ones have been put in an underground repository where nearly 3000 people were killed.

The transfer took place early Saturday morning, with a sombre procession departing from the New York Medical Examiner’s Office on Manhattan’s East Side.

Fifteen vehicles from the New York Police Department, the Fire Department and Port Authority of New York and New Jersey formed the cortege.

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.

Relatives of victims awaited their arrival at the Memorial Museum.

Of the 2753 people declared missing at the World Trade Center site, 1115 – or about 40 per cent 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 7930 could not be matched with the DNA of relatives of the victims.

One group of relatives at the site gathered to protest the move.

“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 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.

The 9/11 Memorial Museum above it will open to the public on May 21 although authorities have set aside five days beforehand for families of the victims, World Trade Center rescue and recovery workers and survivors of the attack.