Speaking at the UN General Assembly session, Viktor Yushchenko said: "Ukraine strongly condemns the violation of Georgia's territorial integrity and the sanctity of its borders, and the armed annexation of its territory."
Yushchenko said the use of force and the resurgence of Cold War-era rhetoric have caused deep concerns in Kiev and "pose a potential threat to Ukraine and other regional states."
Moscow's offensive in response to Georgia's attempt to retake South Ossetia last month and its subsequent recognition of the rebel regions' independence have affected Ukraine, where divisions on Russia's policy in the Caucasus contributed to the breakup of the ruling coalition last week.
Ukraine, which could face a snap parliamentary poll as a result, is also nervous about its Crimea autonomous region, which is populated mainly by ethnic Russians and hosts Russia's Black Sea Fleet base.
Georgian President Mikheil Saakashvili spoke at the General Assembly earlier Wednesday urging a "UN conflict resolution process" for the "peaceful reunification of all parts of Georgia."
Relations between Russia and the two ex-Soviet republics have strained in recent years over a host of issues, including energy supplies and the pair's drive to join NATO and the European Union.
Western powers criticized Russia for attacking Georgia and recognizing the rebel territories. NATO countries, however, remain divided on whether to formally set Tbilisi and Kiev on the path to joining the military bloc.