The fire may have been smoldering for quite some time before construction workers discovered it at 7:15 Saturday morning.
Within five minutes over a dozen units responded to Ground Zero to battle the high rise blaze at One World Trade Center.
It started on the 89th floor and spread to the 90th and 91st.
"The news here is that there were thankfully no injuries, no structural damage to the building," said Port Authority Executive Director Pat Foye.
"And work on One World Trade Center continues."
Construction workers helped firefighters put out the flames.
Fire marshals are still trying to determine the cause.
While it may have been a routine fire, officials acknowledge there was a delay in putting it out, because the building is still under construction.
It uses a dry standpipe system, which means water has to be pumped up from the ground all the way up to the 89th floor.
"It took two pumpers operating for some period of time to get water to that height, with the necessary pressures we required to extinguish the fire, said FDNY Chief James Esposito.
Officials say the building will actually be safer once it is occupied and a so-called wet standpipe system is in place.
"Once the building is completely finished, we'll have water in the standpipe system," said Esposito. "We'll have fire alarm systems, we'll have smoke detectors.
Until then the FDNY will inspect One World Trade Center every 15 days.
The last inspection occurred just 3 days ago.
The rules were put in place following the deadly Duetsche Bank fire in which standpipes had been tampered with.
The new safety practices will continue while the city's tallest building grows taller.
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