Merkulov said: "We have information that the operations conducted in Chechnya that were aimed at counteracting federal actions were planned and carried out with the direct participation of the terrorist Abu Hafs."
He said Abu Hafs had also planned "bandit operations" in Dagestan.
One FSB officer was wounded in the operation, said Irina Volkova, a spokeswoman for the service.
In Moscow, the FSB's central headquarters said in a statement that Abu Hafs' presence in Dagestan signaled that he may have been seeking to flee Russia, and called his death a "telling psychological blow to all the fighters remaining in the North Caucasus mountains".
At least one rebel-linked Web site, daymonk.org, said five militants had been killed in a battle in Khasavyurt, but made no mention of Abu Hafs.
In a recent interview with Vakit, a Turkish newspaper, Abu Hafs said that the Chechnya's struggle for independence from Russia was continuing, despite a reduction in fighting.
In the interview published in November, he said: "The struggle in Chechnya has strengthened. The Russians are not accomplishing more success; success has turned to us.
"Shortly we shall show to the Ummah the real force and power of resistance. Also we shall apply a new strategy ... Now we cause significant losses to the Russians every day.
"We have sent a lot of Russian soldiers to Hell and will be sending many more during our large operations under our new strategy that will soon be applied."
During the early 1990s foreign Muslims - and particularly Arabs - played an important role in the Chechen's war against Russia.
But in recent years, as large-scale fighting has ebbed, the number of foreigners fighting there has dropped.
Russian forces have killed or captured a number of senior Chechen rebel leaders in recent years, including Shamil Basayev, Ibn Khattab and Abdul-Khalim Sadulayev, who was the one-time president of the separatists' self-declared government.
Russian security officials say Abu Hafs took over as al-Qaeda's top emissary in Chechnya in 2004 after the death of Saudi-born chief Abu Walid.