Speaking during his first major news conference at the Skolkovo research hub near Moscow, Medvedev said that European integration was a "normal path" for Ukraine.
"But if Ukraine chooses that path, it will be difficult for it to [integrate] with the common economic space [between Russia, Belarus and Kazakhstan] and the Customs Union," Medvedev said, RIA Novosti reported.
"One cannot sit on two chairs at the same time," he added.
Ukrainian President Viktor Yanukovych has pledged to maintain good relations with both Russia and the West. He has been trying to secure Ukraine an associate membership in the EU and sign a free trade zone agreement with the Customs Union.
Yanukovych has said Ukraine would craft its relations with the Customs Union in a 3+1 format, which will contribute to European and Eurasian economic integration.
Russian energy giant Gazprom has estimated that Ukraine could save $8 billion a year on gas tariffs in it joins the Customs Union, but the Ukrainian constitution prohibits the country from participating in any international alliances.
Medvedev also said during the news conference that Moscow was ready to consider Ukraine's proposals related to prices for gas supplies from Russia.
Yanukovich has long urged Russia to review the "unfair" pricing formula stipulated in the 2009 contract, but talks have yielded little success.
In line with the formula, Russia sells gas to Ukraine at international prices. As a close ally of Russia, Ukraine had previously received a discount on Russian gas.
In April 2010, Ukrainian state energy company Naftogaz and Gazprom signed an additional agreement with a discount of $100 per 1,000 cubic meters of Russian gas in exchange for Ukraine's agreement to extend Russia's lease on a naval base in Crimea until at least 2042.
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