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.
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