"The Georgian side's efforts to increase military potential is causing concern, and I think those initiatives could have bigger consequences than what we saw in August," Serdyukov told a news conference in Ankara.
Russian troops poured into Georgia in August and pushed government troops back after they tried to retake the breakaway region of South Ossetia.
Russia and Georgia have accused each other of starting the five-day war in which Russian forces took control of large swathes of Georgian territory for some time.
Moscow is incensed by the pro-Western course taken by Georgia and particularly its drive to join NATO.
Serdyukov, who was in NATO member Turkey to discuss military cooperation, repeated that Moscow remained opposed to U.S. plans to deploy a radar in Poland and interceptor missiles in the Czech Republic as part of a proposed missile-defense shield.
"Efforts to build air defenses in Poland and in the Czech Republic have awakened concerns, and this is causing Russia to take similar initiatives," he said.
U.S. President-elect Barack Obama, meanwhile, has called Georgian President Mikheil Saakashvili to assure him of Washington's continued support, Saakashvili's press service said Tuesday.
"The conversation was friendly and touched upon future relations between Georgia and the U.S.," the press service said in a statement posted on the presidential web site.
"Obama underlined that he supports Georgia's territorial integrity and paid attention to the importance of continuing reforms in Georgia," it said. "Obama expressed the hope that the two leaders would meet in the near future."
Tbilisi's UN ambassador, Irakli Alasania, said Monday that he expected Obama would maintain strong U.S. support for Georgia's NATO ambitions. But he acknowledged that it might take longer than previously expected for Georgia to get a formal invitation to join NATO.
Alasania was also asked about media reports that monitors with the Organization for Security and Cooperation in Europe present at the time when war broke out have questioned Georgian claims that Russia, not Georgia, started the war.
Alasania said Tbilisi wanted an international investigation of the outbreak of violence in August. He said he stood by Georgia's position that Russia had provoked the conflict.
Separately, human rights group Amnesty International said Tuesday that lootings and kidnappings along Georgia's de facto border with South Ossetia are stopping more than 20,000 people from returning home.
"A new twilight zone has been created along the de facto border between South Ossetia and the rest of Georgia, into which people stray at their peril," said Nicola Duckworth, Amnesty's Europe and Central Asia program director.
"Looting, shooting, explosions and abductions have all been reported in the last few weeks," Duckworth said in a statement accompanying an Amnesty report, released Tuesday, on the war in August between Georgia and Russia.
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