Nearly 8,000 unidentified human remains belonging to 9/11 victims were moved from the city's medical examiner's office to a repository at the Ground Zero museum today, a controversial move that's sparked protest from some family members.

Thousands of remains had been harbored at the ME's office since the 2001 attacks, with officials attempting to identify the fragments and return them to the families. Though the ongoing identification process will continue—"Our commitment to return the remains to the families is as great today as it was in 2001," Mark Desire, who works with the ME's office, told NBC News—the city had always planned to return them to the site. Three coffins draped with American flags were transported via FDNY, NYPD and Port Authority cars to Ground Zero this morning, flanked by policemen and firefighters. They were then interred in a repository in the bedrock of the Ground Zero museum's building, where they will be accessible only to family members and the medical examiner's office.

Some family members supported the move. "I'm fine with the fact that they will be placed in a repository at bedrock," Lee Ielpi, whose firefighter son died in the attacks, told Newsday. "We show the nation—the world—that this is the way we treat our dead: in a respectful way, in a procession, brought back there."

Others, though, have voiced concern and distress over moving remains underground, and this morning some family members showed up at the site with black cloths over their mouths in protest. "Don't put them in the basement," Rosemary Cain, who lost her firefighter son on 9/11, said at another protest on Thursday. "Give them respect so 3,000 souls can rest in peace."

The National 9/11 Museum will open to the public on May 21st; families of victims are invited to visit this Thursday.