Lithuania said it had complained to the European Commission about the Russian gas giant's grip on supply and distribution in the Baltic state, charges that Gazprom denied.
"The Ministry of Energy of the Republic of Lithuania launched a complaint to the European Commission requesting it investigate the abuse of a dominant position by the Russian gas supplier, Gazprom," the ministry said in a statement.
Lithuania has already clashed with Gazprom, and German partner E.ON Ruhrgas, over plans to separate their gas transport and supply assets according to EU energy policy.
The Lithuanian plans mean Gazprom would have to give up ownership of the country's pipeline system.
The EU's 27 members reached a deal on liberalising energy markets in March 2009. They agreed to split giant utilities' supply networks for gas and power from their production assets to help smaller players compete more fairly.
Russian Prime Minister Vladimir Putin in November intervened on behalf of Gazprom, saying the EU rules were uncivilised "robbery".
Energy Minister Arvydas Sekmokas said Gazprom wanted to prevent the emergence of competition in the Lithuanian market.
"The situation where a fully-fledged EU member state is subject to pressure by the monopoly of a third country just because of a determination to implement the fundamental principles of the EU [...] has no equal precedent," he said.
Foreign gas companies have said Lithuania will face supply problems if it goes ahead with seperating supply and distribution, or unbundling, which they regard as unfair.
Gazprom denied the charges on Tuesday, saying it stuck to Lithuania's laws and a mutually agreed pricing formula for gas supplies.
"This market-based approach to price formation has worked successfully in Europe for over 30 years and the claims that it leads to abusive behaviour by Gazprom are simply incorrect," Gazprom spokesman Sergey Kupriyanov said in a statement.
"Gazprom is prepared to deal with any eventuality."
Gazprom owns 37.1% of Lithuanian gas company Lietuvos Dujos and E.ON has 38.9%. The state has 17.7%.
As the Lithuanian row flared up, an oil dispute between Russia and Belarus drew near a settlement.
Moscow was set to resume oil supplies to Minsk by the end of Tuesday, ending a price row which has left Belarus without oil since the start of 2011.
(EurActiv with Reuters.)