"The document has been signed," Vladimir Chizhov said.
Russia earlier said it was ready to restore gas supplies to Ukraine once the new transit control deal had been signed.
European Union energy commissioner Andris Piebalgs, Russian Deputy Prime Minister Igor Sechin, in charge of Russia's fuel and energy sector, and energy giant Gazprom CEO Alexei Miller participated in the signing ceremony.
Gazprom deputy CEO Alexander Medvedev said Sunday Russian gas supplies to Europe, halted last Wednesday over a gas dispute with Ukraine, could resume early Tuesday.
"Deliveries of Russian transit gas [to Europe through Ukraine] could start at 8 o'clock in the morning CET [07:00 GMT] on Tuesday," Medvedev said.
Russia cutoff shipments to Ukraine after talks on outstanding debt and a gas price for 2009 broke down on New Year's Eve. The gas conflict led to a complete break in Russian gas supplies to Europe via Ukraine, which transits around 80% of Russia's gas exports to EU countries.
The European Commission said earlier some 20 countries had been affected by the Russia-Ukraine gas row, especially in the Balkan region, "where the crisis has left tens of thousands of households in the cold and forced schools, hospitals and factories to close."
A gas pricing row between the former Soviet neighbors in 2006 also led to disruptions in shipments to some European consumers, and the latest spat has reawakened concerns about the reliability of Russia as a supplier.
Russian Prime Minister Vladimir Putin said Monday that Gazprom would resume the flow of gas to Europe via Ukraine once it was sure that international monitors were in place to fully supervise the process.
What will be the result of the current Russian-Ukrainian ‘gas war'? (Poll)