A statement from Yushchenko's office said the two leaders discussed the standoff and that Ukrainian Fuel and Energy Minister Ivan Plachkov will travel to Moscow tomorrow for more talks on the dispute.
The call came as Russia's state-run gas firm, Gazprom, seeks to raise its gas prices to Ukraine nearly five-fold next year.
Ukrainian Prime Minister Yuriy Yekhanurov today said Ukraine has the "unquestionable" legal right to take 15 percent of Russian gas shipments passing through its territory as a transit fee.
Gazprom said Yekhanurov's remark was irresponsible and ignorant.
Also today, Russian Defense Minister Sergei Ivanov warned Ukraine not to change the terms of Moscow's lease of a naval base in Ukraine.
"The agreement on the division of the Soviet Union's Black Sea Fleet is an inseparable part of a larger Russian-Ukrainian treaty, the second part of which contains recognition of each other's borders,” Ivanov said. “Therefore, in my opinion, attempts to revise that treaty would be fatal."
Ukraine has suggested charging Russia a higher price for using the Sevastopol base in Crimea.