"Today, on October 1, we legally extended the current treaty for another 10 years. Both Ukraine and Russia realize the importance of the principles outlined in the treaty for the development of our bilateral relations," Yushchenko said in an interview with the Swedish Dagens Nyheter newspaper.
The treaty was to expire April 1, 2009. The agreement is automatically extended for another 10 years if neither side voices the desire to stop it six months prior to the expiration date.
Yushchenko said Ukraine intends to build its relations with Russia on the principles of good-neighborliness, equality and respect for achievements of each nation's independence.
At the same time, the Ukrainian leader said Ukraine and Russia had differing views on the future of European and Euro-Atlantic security.
The recent conflict between Russia and Georgia brought relations between Moscow and Kiev to their lowest point. Ukraine joined the West in accusing Russia of using excessive force in its response to Tbilisi's attack on South Ossetia.
Yushchenko, whose ambition to take his country into NATO is shared by Georgian President Mikheil Saakashvili, said in August that Russia's decision to recognize the independence of Abkhazia and South Ossetia constituted a threat to European security and blamed Russia for the "bloodshed in the region."
However, Russia accused Ukraine of supplying Georgia with heavy weaponry, including tanks and multiple-launch rocket systems, which were used in its attack on South Ossetia in August.
Yushchenko has also signed a decree stating that Russia has to notify the Ukrainian authorities of all movements by naval vessels and aircraft from its Crimea-based Black Sea Fleet.
Ukraine even suggested it could refuse to allow Russian vessels involved in the operation in Georgia to return to the Sevastopol naval base, although the threat was not acted upon.
Russia's Black Sea Fleet uses the Sevastopol base under agreements signed in 1997. Yushchenko announced earlier this year that Ukraine would not extend the lease beyond 2017.