A construction worker found the remains during a routine excavation near a power cable in a manhole located at Ground Zero, the site of the collapsed World Trade Centre.
Workers from utility company Consolidated Edison (Con Ed) then went on to find more human remains, said company spokesman, Steve Coleman.
"The remains were found following the removal of materials from manholes that had been inaccessible since 9-11," Consolidated Edison said in a statement.
The company said it was assisting police and the medical examiner's office in connection with the discovery.
"We share the great sensitivity felt by families and rescuers associated with the tragedy, since many of our employees have been personally involved in the restoration and recovery efforts," Con Ed said.
Discovery fuels anger
The latest discovery has further angered families of victims.
The World Trade Centre Families for a Proper Burial expressed its "outrage at the continued cavalier attitude toward the retrieval of human remains."
The group called on authorities "to complete a thorough search for all human remains, keeping in mind that there are still 1,151 victims for whom there are absolutely no remains."
The latest discovery comes in the wake of the unearthing six months ago of bone fragments found on the roof of the condemned Deutsche Bank skyscraper, which was damaged in the attacks.
The discovery comes just weeks after the fifth anniversary of the suicide plane attacks on the twin towers that left 2,749 people dead.
In total nearly 3,000 people died when hijackers crashed planes on the World Trade Centre, the Pentagon and a Pennsylvania field.