Russia's communications regulator Roskomnadzor accused the network of "censorship" and violating "the rights and freedoms of Russian citizens".
acebook said it had refused to stop fact-checking and labelling content from state-owned news organisations.
Sir Nick Clegg, vice-president of global affairs at Meta, said Russian authorities "ordered us to stop the independent fact-checking and labelling" the outlets' content.
"We refused," he said.
But he made clear he wanted Russians to continue to use Meta's platforms.
"Ordinary Russians are using our apps to express themselves and organise for action", Sir Nick said, and the company wants "them to continue to make their voices heard".
Many state-owned media outlets in Russia have painted a largely positive picture of Russian military advances in Ukraine, calling the invasion a "special military operation" that had been forced on Moscow.
On Thursday Meta said it had set up a "special operations centre" to monitor content about the conflict in Ukraine.
