A fire has destroyed part of a chemistry laboratory at the Australian National University (ANU).

Emergency authorities were called to the fire around 1:00pm AEDT to find the Birch Building filled with smoke, and a room on the third level ablaze.

It is believed the fire started during science experiments in a fume cupboard, before spreading into the roof.

Fire and Rescue Commander Danny Brighenti says initial fire fighting efforts were hampered because it was unclear whether chemicals were present.

"We couldn't use water until we contained the fire, then realised the chemicals weren't in the area, then we could go back to normal fire fighting procedures," he said.

ANU vice-chancellor Ian Young says he is confident all correct protocols were in place at the laboratory.

"I have no reason to believe there was anything inappropriate or not following the necessary protocols. We really don't know exactly how the fire started at this stage," he said.

More than 100 people were evacuated and a 44-year-old man was treated for smoke inhalation.

The ANU says it is too early to say how much damage the fire has caused.