Russia's Investigative Committee said suspects Bakhram Ergashev, Ibragimzhon Ermatov and Makhamadyusuf Mirzaalimov had been charged with involvement in a "terrorist act" and for having illegally used explosives.
Seven other suspects in the April 3 attack, which killed 15 people, will be charged in the near future, the committee said.
The Imam Shamil Battalion, a group suspected of links to Al-Qaeda, claimed responsibility for the bombing, US monitor SITE Intelligence Group said last month.
In a statement by the group cited by SITE, it said the bombing served as a message to Russia and countries engaged in war with Muslims that the "price" of that war was "expensive".
Russian authorities have attributed the attack to 22-year-old Akbarjon Djalilov, thought to be a Russian national born in Kyrgyzstan, who died in the blast.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)
Get the latest election news, live updates and election schedule for Lok Sabha Elections 2019 on ndtv.com/elections. Like us on Facebook or follow us on Twitter and Instagram for updates from each of the 543 parliamentary seats for the 2019 Indian general elections.