Russia's FSB security agency has said the Telegram mobile messaging app was used by a suicide bomber who killed 15 people in St Petersburg in April.
Authorities have already threatened to block the app, founded by Russian businessman Pavel Durov, for refusing to sign up to new data laws.
Mr Durov has refused to let regulators access encrypted messages on the app.
Telegram has some 100 million users and has been used by so-called Islamic State (IS) and its supporters.
IS used the app to declare its involvement in the jihadist attack on and around London Bridge in the UK last month.
Telegram has been used by jihadists in France and the Middle East too, although the app company has highlighted its efforts to close down pro-IS channels. Telegram allows groups of up to 5,000 people to send messages, documents, videos and pictures without charge and with complete encryption.
Now the FSB has said that as part of its investigation into the St Petersburg attack it "received reliable information about the use of Telegram by the suicide bomber, his accomplices and their mastermind abroad to conceal their criminal plots at all the stages of preparation for the terrorist attack".
A Russian identified as Akbarzhon Jalilov blew himself up between two underground stations on 3 April. The security agency said that Telegram was the messenger of choice for "international terrorist organisations in Russia" because they could chat secretly with high levels of encryption.
The FSB's revelation made no mention of a threat on Friday by Russia's communications regulator Roskomnadzor to block the app over its failure to register Telegram as a disseminator of information in Russia. By registering, the company would have to store the past six months' of users' data in Russia.
Mr Durov has complained that the regulator also asked Telegram to hand over encryption keys so they can read users' correspondence to catch jihadists.
He argues that it would be against the Russian constitution and the owners do not have access to the encryption keys anyway.
Several internet companies have been criticised beyond Russia for allowing jihadists to spread material about bomb-making and incitement.
Last week, the European Union's 28 leaders agreed to put legal pressure on internet giants like Google, Twitter and Facebook to remove jihadist content more quickly and to develop tools to help detect incitement to terrorism online.
The messenger Russia wants to ban - by Vitaliy Shevchenko, BBC Monitoring
Russia is threatening to ban the Telegram after its founder refused to co-operate with the country's security services.
Mr Durov was also founder and CEO of Russia's most popular social network VKontakte (VK). But in 2014 he was forced out of the company after refusing to hand over user data to the security services. He left Russia shortly afterwards.
Telegram has been gaining in popularity as a news-sharing platform in Russia's tightly controlled media environment, and some fear that banning it would further restrict freedom of speech there.
Social media users have suggested that it is absurd to try to ban something useful just because it is being misused by criminals. "Terrorists use physics and chemistry. Let's ban physics and chemistry," quipped one Tweet.
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