The remains left the Office of the Chief Medical Examiner on Manhattan's East Side shortly before 7 am in three city vehicles. They were accompanied by police and fire department vehicles with lights flashing but no sirens.
Construction workers paused as the motorcade passed, and about 10 firefighters stood in the cool breeze saluting the vehicles as they arrived. The remains will be transferred to a repository 70 feet (21 meters) underground in the same building as the National September 11 Memorial Museum.
Like many decisions involving the site of the worst terrorist attack in the US the disposition of the unidentified remains has been contentious.
A group of victims' family members who say the remains should be stored in an above-ground monument separate from the museum protested the procession. About a dozen wore black bands over their mouths at the site Saturday.
"It's horrible. I am so angry. I am so angry. I am outraged,'' said Sally Regenhard, whose firefighter son was killed at the trade center.
"The human remains of my son and all of the 3,000 victims should be in a beautiful and respectful memorial, not in the basement of a museum,'' she said.
Rosemary Cain, who also lost her firefighter son at the trade center, was also upset about the transfer.
"I don't know how much of him is down here; if it's one little inch, I want it treated respectfully,'' she said. "I want it above ground. I don't want it to be part of a museum. I don't want it to be part of a freak show.''
Other family members support the plans, which have been in the works for years. Lisa Vukaj, who lost her 26-year-old brother, said the new home for the remains is "a fitting place until technology advances'' and new techniques are available to identify their loved ones.
Vukaj, who got emotional as the flag-draped caskets were taken inside the center, said she didn't like that some victims' relatives turned what should have been a solemn event into "a political thing.''
"Just come in, pay your respects, be here, have your emotions and don't make it political,'' she said.
Uniformed officers from the New York Police Department and Fire Department of New York and the Port Authority police carried the three caskets into the repository.
The facility will be available for family visits but will be overseen by the medical examiner. Officials hope that improvements in technology will eventually lead to the identification of the 7,930 fragmentary remains.
The death toll stemming from the attacks at the World Trade Center stands at 2,753. Of those, 1,115, or 41 percent, have not been identified.
Monica Iken-Murphy, whose husband was a bond broker in the North Tower, said she hopes his remains will eventually be identified.
"Every year they identify someone,'' she said. "Last year they identified a male and female in their 40s. I could be next, and I'm optimistic that he could be one of those. Even if he isn't, I feel he is home. This is where he took his last breath, his last step. This is where he lost his life.''