"We will give priority to supplying those countries that have suffered the most from the conflict - namely, the Balkan states and Slovakia," Vladimir Putin said during a visit to Gazprom's control center with the energy giant's CEO, Alexei Miller.
Miller said Ukraine had refused on Tuesday to meet Gazprom's request to pump 22.2 million cubic meters of gas to Slovakia.
Putin is due to hold emergency gas talks with his Bulgarian and Slovakian counterparts in Moscow on Wednesday.
"I have just spoken to prime ministers of Bulgaria and Slovakia. We agreed to meet in Moscow tomorrow," he said.
Gazprom gave the go-ahead on Tuesday morning to resume pumping gas via Ukraine but no gas got through to Europe, causing Moscow to accuse Kiev of blocking gas transit.
Miller told Putin that Ukraine's Naftogaz energy company had no reason for refusing to transit Russian natural gas to Europe.
"There can be no reasons, this is gas feeding into the export gas pipeline, deliveries should be made by direct transit," Miller said.
Naftogaz head Oleh Dubyna said his company was unable to meet Gazprom's proposal to transit 76 million cubic meters to Europe since that would disrupt gas supplies to Ukrainian consumers, specifically in the Odessa, Luhansk, Donetsk and Dnipropetrovsk regions.
Ukrainian President Viktor Yushchenko denied earlier on Tuesday that Kiev was blocking Russian gas transit to Europe or stealing gas, following a failure by Russia to make a test delivery through Ukraine.
"Ukraine has not tapped a single cubic meter of gas either in 2009 or 2008," Yushchenko said.
He said Ukraine remained open to talks on gas supplies from Russia and did not owe anything to any Russian company, saying final payments on the country's 2008 gas debt had been made in late December with an advance payment for January supplies.
According to Gazprom, Ukraine still owes $614 million after paying $1.5 billion.
President Dmitry Medvedev told Yushchenko on Monday that Russia was ready to resume talks without delay between Gazprom and Naftogaz on a contract for Russian natural gas deliveries to Ukraine in 2009, adding that the gas would be delivered at market prices.
Gazprom earlier said that as Ukraine had refused a preferential price of $250 per 1,000 cubic meters it would now have to pay "the average European market price of $450-470."
However, Yushchenko's energy security envoy Bohdan Sokolovsky said on Monday that in that case Ukraine would have to significantly raise its gas transit fees - from the current $1.7 per 100 kilometers to "an average European rate" of $4.7.
Yushchenko said on Tuesday that "in theory" the transit fee could be as high as $10.
He added that Russia had launched a targeted campaign against Ukraine in a bid to seize control of its gas transit system.
The move to resume gas supplies to Europe was made after Russia, Ukraine and the EU signed a deal on Monday allowing the presence of international monitors at Ukrainian and Russian gas transportation facilities to oversee gas transit.
Russia halted gas supplies to Europe on January 7, accusing Ukraine of tapping transit gas. Moscow cut off gas deliveries to Ukraine on January 1 after the parties failed to agree on Kiev's debt for supplies in 2008 and a price for a 2009 contract.