Arson probers said no one was hurt in the fire which started at the fourth floor of the Soledad Building located along Pureza street, Ramon Magsaysay Boulevard in Sta. Mesa at 3 a.m.
The NSOs cash division and National Capital Region (NCR) operations center are housed in the building.
The fire reached the fifth alarm before it was placed under control at 5 a.m.
Firefighters had to use high-rise ladders to scale the burning building. Thick smoke filled all floors of the building, hampering the firefighters efforts to contain the blaze.
Investigators said the fire could had been ignited by the sudden surge of electric power.
The building had been without power for two days as a result of Typhoon Milenyo last Thursday.
Damage to property could reach P1 million even as NSO officials are still conducting inventory of equipment, arson probers said.
NSO officials said documents, including birth certificates and marriage contracts, were not destroyed because they had long been transferred to the NSOs Quezon City office.