Pretoria town clerk Henry Enslin said the committee hearings would not be able to continue in the Munitoria complex on Tuesday.
The entire west wing of the complex, housing the city council's tax, licensing and water and electricity departments was destroyed by the fire and firemen were still fighting the blaze late on Monday night.
Although the room in which the hearings were held did not burn, city council spokesman Tommy Thomson said the committee's sound and translation equipment was damaged, apparently by water and smoke.
Further testimony about the killing of a policeman said to have been an ANC spy was expected on Tuesday.
Amnesty for the killing of Sgt Richard Motasi and his wife Irene in the eighties is being applied for by Capt Jacques Hechter and W/O Paul Janse van Vuuren, two of five former security policemen applying for amnesty.
Amnesty applications by a large number of other former security forces members are to be heard this year.
Hechter on Monday said the Motasis were shot dead at their Hammanskraal home because Sgt Motasi was giving information to the Zimbabwean secret service.
Van Vuuren said information was received that Motasi was also a courier for the African National Congress.
Both allegations would be denied by the victims' family, their lawyer Brian Currin said.
There have been reports that Motasi was actually killed because he was involved in making a civil claim against the police. Hechter and van Vuuren say they heard of this only recently.
The commission, sitting in Pretoria for the past six working days, has completed only two days of scheduled work.
There is talk of extending the hearings beyond the scheduled closing day on Wednesday to the end of the week, but even that may not be enough time to complete the amnesty applications.
Besides Hechter and van Vuuren, the other amnesty applicants are Col Roelf Venter, Brig Jack Cronje and Capt Wouter Mentz.
They were all operatives based at the secret police farm Vlakplaas.