The thefts at the Miramas site, which is operated by a combination of military services west of Marseille, appeared to have occurred overnight from Sunday to Monday. The break-in comes as France has strengthened its security measures after two deadly attacks by extremists this year.
Marseille prosecutor Brice Robin said an investigation has started on charges of "theft with break-in carried out by a criminal group" and "fraudulent entry into a military compound."
An official with the gendarmerie police force, which generally runs law enforcement in more rural areas of France, said the thief or thieves appeared to have cut through a fence to enter the high-security site. The official was not authorized to speak publicly because the operation is ongoing.
Defense Minister Jean-Yves Le Drian said he has ordered an investigation into how the break-in was organized and who might be responsible. He also instructed a new office in charge of protecting such sites to review the security for all French military weapons stocks and propose "corrective measures" within 15 days.
Mayor Frederic Vigouroux of Miramas told The Associated Press it was the first theft at the site. The outer fences were broken into and nine storehouses were affected, he said.
"It wasn't cotton candy that was stolen," he said. "These are dangerous munitions."
France has been on its highest level of alert for terrorism following deadly attacks in January and June.
The 200-hectare (500-acre) base sits on the outskirts of the town of 30,000 and stocks munitions like those used in French military operations in Mali and Afghanistan.