The head of the Russian Federal Security Service (FSB), Nikolai Patrushev, told President Vladimir Putin earlier that a number of militants had been killed in the south Russian republic of Ingushetia, including Basayev.
"Even though special 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.
The DNA test will take around a week, he said.
Basayev, who claimed responsibility for the 2004 Beslan school massacre and a number of other atrocities, was killed in a car accompanying a truck carrying explosives, police said earlier.
"Basayev's body was found by FSB officers after a car wired with explosives blew up. The convoy included three cars with militants, one of which was Basayev... The terrorist was decapitated by the explosion, but from characteristic traits, it was suggested that the body was none other than Shamil Basayev," police said.
After initial examinations, the terrorist's identity was confirmed, he said.
The siege of a school in Beslan in the southern Russian republic of North Ossetia in September 2004 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.
In all, 147 people, mostly civilians, died.