The university says construction work was the cause and that it was "accidental."
The town of Villeurbanne, the Lyon suburb where the university is located, tweeted that the area has been evacuated after Thursday's blast. It said the explosion hit the roof of the building.
An official with the Lyon region emergency service said firefighters are on the scene.
The explosion hit days after a blast apparently caused by a gas leak hit a Paris bakery, killing four people and injuring several.