The warehouse in Bobigny, north east of the capital, had been rented by a man suspected of fraud, reported Le Parisien newspaper.
Shaped like a large container, the command post contained the latest in electronic and computer technology and is estimated to be worth €600,000 ($823,000).
"The command post was destined to be used in the field of battle," according to a source quoted by the newspaper. "It can shelter around ten soldiers. It's not a very discreet item. The mystery is how something like this could have been stolen."
Army sources confirmed that the post had gone missing from its Montlhéry barracks south of Paris in July, but could not say how it had been removed.
Police are yet to discover from the suspect, a 46-year-old man from the Ivory coast, how he got hold of it.
"The suspect being held by police has not explained how he managed to procure the command post," said a source.