"This should be of concern not only for Georgia but also for other regional actors, including Nato," Temur Yakobashvili, Georgia's deputy prime minister, said.
"This is changing the balance of power in the region," he said, adding that it could also be seen as a response to US plans to install a missile defence system in eastern Europe, Russia's traditional sphere of influence.
"The Russian government is saying 'if you can do it, we can do it'," Yakobashvili said.
Russian forces moved into Georgia in August 2008 after fighting broke out in Abkhazia and South Ossetia, prompting the worst post-Cold War crisis between Russia and the West.
Russia subsequently recognised the two regions as independent, but Tbilisi insists that both regions are still an integral part of Georgian territory.
Eka Tkeshelashvili, Georgia's National Security Council secretary, accused Moscow of "strengthening its image and role as an occupying country" with the deployment of the S-300 missile system.
"It shows ... not only that Russia does not intend to withdraw its troops from Abkhazia and South Ossetia, but that it is actually strengthening its military control over these territories."
Zelin said that the missile battery was also aimed at the "destruction of any flying object penetrating into the covered territories, whatever aim they were flying with".
"The task of these air defence systems is not only to cover the territory of Abkhazia and South Ossetia but to avert violations of state borders in the air," he said.
Last weekend, Moscow marked the second anniversary of the outbreak of the war, with Dmitry Medvedev, the Russian president, making a surprise visit to Abkhazia, his first trip since the conflict.
Only Venezuela, Nicaragua and the tiny Pacific island state of Nauru have followed Moscow's move to recognise the independence of Abkhazia and South Ossetia.
The regions, which have long looked to Russia for support, slipped out of Georgia's control in the early 1990s after a series of violent conflicts with separatists.