"Identified among the killed militants were Shamil Basayev, Isa Kushtov, Ali Taziyev, and Tarkhan Gazhiyev," the Federal Security Service (FSB) said.
Basayev had claimed responsibility for the 2004 Beslan school siege and the 2002 Moscow theater attack.
A source with the security services in southern Russia said earlier that after initial examinations, the terrorist's identity was confirmed, but added that Basayev's body would undergo a DNA analysis to prove his identity.
"Even though security forces are 100% sure that Basayev has been killed, his death will be confirmed. The terrorist's remains will be brought to a medical laboratory, where an analysis will be carried out," the source said, adding that the DNA test would take around a week.
The FSB said they had destroyed a convoy of cars with militants.
Earlier FSB reports said the militants had been killed preparing for a terrorist attack when their explosive-laden truck blew up. It later transpired that Basayev had been traveling in one of the accompanying cars.
Ingushetia's Interior Ministry said experts were still working at the scene, defusing unexploded shells in the truck.
As well as the school siege in Beslan in the southern Russian republic of North Ossetia in September 2004, which led to the deaths of 331 people including 186 children, Basayev also claimed responsibility for masterminding the 2002 Moscow theatre siege, which claimed the lives of 130 people. He also led an attack on a hospital in the southern city of Budyonnovsk, where terrorists took more than 1,500 hostages for five days in June 1999.
