About 300 people were in the building at the time, but they were evacuated without any panic.
Bassoonist Stefan Schweigert said the fire brigade had allowed musicians into the building to remove instruments that had been left in lockers overnight - although some, such as pianos, were too large to move.
The extent of the damage is unclear, but fire officials say the fire did not spread through the building.
The hall - a Berlin landmark - was built in the 1960s, and is famed for its acoustics.
Firefighters on the rooftop of the Berlin Philharmonic building trying to put out the fire
Pamela Rosenberg, general manager of the Berlin Philharmonic, told the BBC: "After the war this represented all of the hopes of bombed-out Berlin. It was like the Phoenix rising from the ashes."
She added that the hall "really symbolises Berlin".
The Philharmonic, the city's leading orchestra, is directed by Sir Simon Rattle.
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