The rebels were killed in a shootout with security forces in the Khasavyurt region of Dagestan bordering Chechnya, the committee said in a statement.
One FSB special forces officer was wounded in the shootout in woods near the village of Kurush, it said.
Those killed were identified as "involved in the September murder" of the village's 34-year-old imam Magomed Khidirov, who was shot by masked men as he went to morning prayers.
Dagestan has become a hotbed of Islamic extremism, and moderate preachers are regularly targeted there and in the wider North Caucasus region.
Islamists in the North Caucasus have previously been united under a local Caucasus Emirate organisation, but are now increasingly flocking to Islamic State, which in June declared it had established a franchise there.
Syria's Al-Qaeda affiliate Al-Nusra Front this week called on jihadists from the Caucasus to perpetrate attacks in Russia in response to the air strikes.
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