Joaquin Almunia, vice president for competition policy in the European Commission, said during a summit in Lithuania the Russian company was under investigation.
"We are looking at the business practices of Gazprom, which we suspect of abuses in the supply of upstream gas in Central and Eastern Europe," he said in a statement.
European energy security is threatened by geopolitical rows between Gazprom and Ukraine, whose pipelines carry the bulk of Russia's gas to European consumers.
Almunia said Lithuania, a former Soviet republic, was one of the early countries lodging a complaint against Gazprom though the scope of the investigation has extended across much of the Baltic region.
"We suspect that Gazprom has been hindering the free flow of gas across member states [of the European Union] and the diversification of sources of supply," he said in his address Thursday.
Europe is trying to break the Russian grip on its regional energy sector by courting major natural gas suppliers in the Caspian Sea region.
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