Khadiyev, a militant and Muslim religious leader, had been active in Chechnya and Daghestan since May 2008 reviving separatist groups controlled by Zakayev, the London-based head of the "Chechen government in exile," the Federal Security Service said in a statement.
Russia has repeatedly asked Britain to extradite Zakayev, accused of terrorist activities, but the request has invariably been refused.
"Considering the danger posed by the militant leader, the FSB along with the Interior Ministry conducted an operation to seize him, during which Khadiyev offered resistance, was wounded and died of his wounds," the domestic security service said.
It added that the operation had been carried out on January 17.
"The liquidation of Khadiyev is a serious blow to the bandit underground," the FSB said.
The service also said another two militants had been killed in Ingushetia, on Saturday.
Brothers Ruslan and Murad Uzhakhov, believed to have been involved in a series of attacks on law enforcement officials, were killed in a special operation in the city of Nazran.
