RSF noted with irony that Charlie Hebdo's staff could no longer edit comments on its Facebook "wall", including those inciting violence, while the "enemies of freedom of expression" could continue to post hate messages.
"Facebook has just discovered opportunely that Charlie Hebdo 'is not a real person', something that breaks the site's rules," RSF said in a statement, citing a message in French from Facebook.
"The content that you have published on Facebook has been deleted for breaking (Facebook) rules. Postings with graphic, sexually explicit or excessively revealing content are banned," it quoted Facebook as saying.
"This message is a warning. Another infraction will result in the account being terminated."
Charlie Hebdo -- which on Wednesday published a special Arab Spring edition with Muhammad on the cover as "guest editor" saying: "100 lashes if you don't die of laughter!" -- has the offending cover as its Facebook profile picture.
"We can only regret a position that says the enemies of freedom of expression are right and which leaves us perplexed as to the social network's real motives for closing the account," RSF said.
"The newspaper can no longer either add or block outside comments, be they hateful or threatening, as the page's administrator cannot deactivate outside contributions," RSF said.
"It is extremely worrying to notice that the social network seems to fall on the side of censorship and restricting the freedom to inform," RSF said, noting that Facebook had already closed the pages of several dissidents.
Facebook shut down the page of Michael Anti because it was a pseudonym of Chinese political blogger Jing Zhao, while the Facebook group "We are all Khaled Said", named after an Egyptian blogger killed by security forces, was closed because the group's administrators didn't use their real names.
"If Facebook closes Charlie Hebdo's page it would have far-reaching consequences for journalists, bloggers or internet activists, who may in future censor themselves," RSF said.