Authorities had been hunting for Dmitri Sokolov since the blast in Volgograd, the first attack in years against a civilian target outside the volatile North Caucasus region, which came just months before the start of the 2014 Winter Games in Sochi.
Police surrounded a house in a village near the Dagestan capital of Makhachkala and unsuccessfully tried to persuade the insurgents to surrender before they died, the National Anti-Terrorism Committee said.
It was not immediately clear if the operation was specifically part of a search for Sokolov. Authorities gave few details, and it was unclear how the insurgents died.
Sokolov's mother spoke with him by telephone during the stand-off to try to get him to give up, the committee said. A woman and a child who were in the house when the stand-off began were freed.
An Islamic insurgency has been simmering in the North Caucasus for more than a decade after two separatist wars in Chechnya. In Dagestan, the center of the insurgency, bombings and shootings occur almost daily.
After the bombing, authorities said Sokolov had become a top rebel expert in explosives. The bomb was rigged with shrapnel, which caused severe injuries and left many of the more than 30 wounded in grave condition.
Investigators also believe Sokolov had prepared explosives for a suicide bomber who blew herself up outside the regional branch of Russia's Interior Ministry in Dagestan in May, killing 12 people.
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