"Roskomnadzor has received the ruling of (Moscow's) Tagansky court to block Telegram's services on Russian territory. This information was sent to providers on Monday," the watchdog said in a statement.
Some Russian internet providers began blocking Telegram on Monday afternoon.
"Russian authorities have begun blocking Telegram. The service could be unstable without a VPN. We will inform you on the developing situation," the messaging app notified its Russian users.
Around 10 activists were arrested after demonstrating outside the FSB security service headquarters against the move, Maria Alekhina, a member of the Russian protest punk group Pussy Riot, told Ekho Moskvy radio.
Pussy Riot members were among those arrested, she said.
"The police came and took us by the arm and put us in a van," Alekhina said, adding: "They did not give us a reason."
She said the protesters had flown paper planes -- Telegram's logo -- at the FSB building.
The Kremlin's press service told journalists on Monday that it will be switching to ICQ, a 1990s chat service now owned by billionaire Alisher Usmanov's Mail.ru, to communicate with them.
"It is telling that authoritarian governments (e.g., Russia) are trying to block Telegram over encryption, but are more relaxed when it comes to other encrypted messaging apps," Pavel Durov, the app's maverick creator -- dubbed Russia's Mark Zuckerberg -- wrote on Twitter.
Writing on Vkontakte, the social media platform Durov founded that is now under state control, he said the decision harms Russia's national security as users will switch to WhatsApp and Facebook which are "controlled from the US."
"We believe the ban is anti-constitutional and will continue to defend the right of Russians to private messaging," said Durov, who left Russia in 2014 and is now based in Dubai.
Durov has long said he will reject any attempt by the country's security services to gain backdoor access to the app.
The ban followed a long-running battle between authorities and Telegram, which has a reputation for securely encrypted communications, as Moscow pushes to increase surveillance of internet activities.
Telegram, a free application that lets people exchange messages, stickers, photos and videos in groups of up to 5,000 people, has attracted more than 200 million users since its launch by Durov and his brother Nikolai in 2013.
Telegram is especially popular among political activists of all stripes, but it has also been used by jihadists.
Russia has acted to curb internet freedoms as social media have become the main way to organise demonstrations.