The article on the free online encyclopedia, created in July 2009, dealt with a military radar station in Puy-de-Dome in south-central France.
The Wikimedia Foundation said it was contacted on March 4 by the DCRI, which said the article on the French language Wikipedia "contains classified military information and that publication of such information violates the French penal code".
"The DCRI demanded removal of the article in its entirety," the US-based foundation said on its website on Saturday.
Wikimedia said it refused and asked for more information from the French authorities, which never came.
Then, on March 30th, the DCRI contacted a Wikipedia volunteer in France and "insisted that he use his administrative rights to immediately remove the article, or face serious and immediate reprisals," Wikimedia said.
"Under the shadow of these threats he removed the article."
According to the French interior ministry, the article concerned "the organisation of the national defence's nuclear component".
Wikimedia France said the volunteer, who had nothing to do with the article in question, was threatened with detention and possible charges.
The French ministry however denied making threats, saying it had simply informed the volunteer about "the risk of legal action" against himself and Wikipedia France.
The article has since been restored on the website by a volunteer in Switzerland, according to Wikimedia France.
The non-profit Wikimedia Foundation expressed its opposition to "any governmental attempts to intimidate volunteers" and said it was "certainly sensitive to national security concerns".
But where there is "no apparent threat... we require more information before we will consider removing any content".
"To do otherwise would allow censorship to trump free expression," it added.