No victims were reported, and no sensitive materials or viruses were affected by the fire, which was extinguished by firefighters, an official at the institute said. The official was not authorized to be publicly named according to company policy.
The cause of the blaze was unclear.
The fire broke out mid-morning in an underground level of one of the buildings in the institute's campus in southern Paris, a lab that conducts research in developmental biology, the official said.
The Paris fire department said 17 fire engines were sent to the site. All those inside the lab building were evacuated but were let back in after the fire was extinguished at midday, the institute official said.
The degree of damage was being investigated.
The Pasteur Institute was founded in 1887 by scientist Louis Pasteur. Its Web site says it has 2,600 employees of more than 60 nationalities, and 30 subsidiary institutes around the world.