Fifteen people were killed in the suicide bombing, which was claimed by the little-known Imam Shamil Battalion.
"During the probe into the April 3 terrorist attack in the Saint Petersburg metro, the FSB received reliable information about the use of Telegram by the suicide bomber, his accomplices and their mastermind abroad to conceal their criminal plans," the FSB said in a statement.
They used Telegram "at each stage of the preparation of this terrorist attack," it said.
Fifteen people were killed in the suicide bombing, which was claimed by the little-known Imam Shamil Battalion, a group suspected of links to Al-Qaeda.
Telegram is a free Russian-designed messaging app that lets people exchange messages, photos and videos in groups of up to 5,000. It has attracted about 100 million users since its launch in 2013.
But the service has drawn the ire of critics who say it can let criminals and terrorists communicate without fear of being tracked by police, pointing in particular to its use by Islamic State jihadists.
The FSB charged that "the members of the international terrorist organisations on Russian territory use Telegram".
The app is already under fire in Moscow after Russia's state communications watchdog on Friday threatened to ban it, saying the company behind the service had failed to submit company details for registration.
Telegram's secretive Russian chief executive, Pavel Durov, who has previously refused to bow to government regulation that would compromise the privacy of users, had called that threat "paradoxical" on one of his social media accounts.
He said it would force users, including "high-ranking Russian officials" to communicate via apps based in the United States like WhatsApp.
The 32-year-old had previously created Russia's popular VKontakte social media site, before founding Telegram in the United States.
Durov said in April that the app had "consistently defended our users' privacy" and "never made any deals with governments."
The app is one of several targeted in a legal crackdown by Russian authorities on the internet and on social media sites in particular.
Since January 1, internet companies have been required to store all users' personal data at data centres in Russia and provide it to the authorities on demand.
Draft legislation that has already secured initial backing in parliament would make it illegal for messaging services to have anonymous users.