Maj. Gen. Alexander Rogachyov, 46, was discovered dead in his Toyota Land Cruiser near a restaurant by security guards on Sunday.
According to forensic experts the "death occurred as a result of a gunshot wound to the head," the source said.
Investigators said Rogachyov was shot from close range. The murderer is believed to have been sat in the front of the vehicle next to the victim, when Rogachyov was shot with a 9 mm caliber handgun.
"Experts retrieved a bullet of this caliber from the victim," the source said.
Earlier media reports said the former FSB officer could have died of a heart attack. A criminal case has been opened and an investigation is underway.
In late December, Maj. Gen Valery Lipinsky was fatally injured in an attack on his car in Makhachkala, in the southern Russian republic of Daghestan.