The body of Eduard Emin-zade, chief of the counterintelligence department at the Abkhazian Defense Ministry, was discovered in a house in the Gali district of Abkhazia with a gunshot wound to the head.
A team of investigators later found the body of the owner of the house in a roadside ditch 500 meters from the nearby Ingur checkpoint.
Emin-Zade survived an assassination attempt in June when he and his driver were seriously injured in an attack on their vehicle near a railway station in the Abkhazian capital of Sukhumi. The assailants were never brought to justice.
Abkhazian President Sergei Bagapsh is currently holding an emergency meeting with the republic's senior security staff over Emin-zade's death, the source said.
Russia recognized Abkhazia and another Georgian rebel republic, South Ossetia, as independent states on August 26. So far, only Nicaragua has followed suit.
The move came after a five-day war between Russia and Georgia that began when Georgian forces attacked South Ossetia in a bid to regain the breakaway province.