Baluyevsky drew a parallel between the future of Serbia's Kosovo province and the breakaway regions, which are seeking international recognition as independent states.
"Georgia at the moment is in a state of confusion, because if the Kosovo problem is settled by giving Kosovo sovereignty, then Georgia could lose Abkhazia and South Ossetia," he was quoted as saying.
Georgian investigators identified the weapon as a Russian-made Raduga Kh-58 missile, designed to hit radars, Georgia's foreign ministry said on Wednesday.
The missile missed its target because Georgia's military switched off the radar after it had detected the intrusion and the missile's launch.
"We switched the radar off, so that the missile wouldn't home in on it," Colonel Zurab Pochkua, a defence ministry spokesman, said on Thursday.
Tbilisi has described the missile incident as an "act of aggression" by Russia, and has requesting a special meeting of the UN Security Council concerning the matter.
Russia has denied dropping the missile and its officials have suggested Georgia may have planted the missile to provoke tensions with Moscow.
The United States on Wednesday condemned what it termed "a rocket attack" against Georgia.
"The US condemns the August 6 rocket attack against Georgia," Sean McCormack, state department spokesman, said in a statement issued on Wednesday.
"We praise Georgia's continuing restraint in the face of this air attack and call for the urgent clarification of the facts surrounding this incident."
McCormack appealed to Russia and Georgia resolve their differences over the South Ossetia.
"The proximity of this attack to Georgia's separatist South Ossetia region and the violation of Georgia's airspace over the zone of conflict underscore the pressing need for progress toward peaceful resolution of the South Ossetia conflict," McCormack's staetement said.