"The plane has been shot down. Now efforts are under way to find its fragments," Bagapsh said.
The Abkhaz president said Abkhazia had informed the peace-keeping forces in the region about the incident, adding that similar violations by Georgia had also been registered previously.
Meanwhile, the Georgian Defense Ministry rejected on Sunday its complicity in the incident, saying that Georgian planes had not performed any flights over the territory controlled by Abkhazia.
Georgia is seeking to regain control of Abkhazia and South Ossetia, which proclaimed independence following the break-up of the Soviet Union in 1991.
Ex-Soviet breakaway regions have stepped up their drive for independence since Kosovo's declaration of independence on February 17. Abkhazia and South Ossetia, along with Moldova's Transdnestr, have since asked Russia's parliament, the United Nations and other organizations to recognize their independence.