"The fact that around 200 fighters from Russia are fighting on the side of the Caucasus Emirate under the flag of Al-Qaeda and other related structures provokes concern in Russia," the head of the FSB Alexander Bortnikov said at an international security forum in the central Russian city of Kazan.
Russia opposes foreign military intervention in Syria which President Vladimir Putin said this week was "doomed to failure" and it is urging both sides to attend a peace conference in Geneva.
Russia sees almost daily attacks by insurgents in its North Caucasus region, targeting the Moscow-backed authorities, while security forces regularly kill suspected rebels in operations.
Russia is a key ally of President Bashar al-Assad and has used its veto against United Nations Security Council resolutions calling for sanctions against his regime.
Bortnikov said that he believed that the number of rebels going to Syria from Russia was growing.
He also warned that such fighters would gain battlefield experience in Syria and present a greater danger on their return home.
"The danger is that in the end these terrorists will return to the countries where they came from. What can we do and what barrier can we put up against the plans and intentions of those who have been 'broken in' and learnt to fight, so as not let them back into their own country? This question was actively discussed," he said.
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