Charges from the European Commission that energy company Gazprom abused its market position are "absolutely inadmissible," Russia's foreign minister said.

Markets rules in the Europe discourage energy companies from controlling both transit arteries and the reserves they carry. Margrethe Vestager, the European commissioner in charge of competition policy, said Gazprom was "abusing its dominant position" in the European market.

Gazprom in a Wednesday statement said the charges are baseless, adding it "strictly" follows the rules of the countries in which it operates.

Russian Foreign Minister Sergei Lavrov said the Kremlin was confident both sides could resolve the issue, but noted the government would work in defense of Gazprom's interests.

"The argument is simple: all the contracts, which Gazprom signed with its partners, were concluded in full compliance with the legal regime that existed in the European Union at that time," he said. "This [set of charges] is absolutely inadmissible."

Lavrov said Gazprom contracts predate European laws that restrict the role energy companies play in the regional market. The European Commission, he said, is trying to regulate anti-trust issues retroactively.

Most of the Russian gas headed to the European market runs through a Soviet-era transit system in Ukraine, where lingering conflict and contractual rows between Kiev and Gazprom add a layer of risk to European energy security.

Europe is looking to Azerbaijan as a source of diversity, while Russia aims to build a new gas artery through Turkey that would circumvent geopolitically sensitive territory in Ukraine.

Vestager said the complaint does not extend to the Ukrainian market, but to other markets where Gazprom is the only gas supplier.

"This may be seen by some as a more political case than some of the other competition cases in my portfolio," she said. "But if you dig into past case files, you will actually find other companies, which we have investigated under EU antitrust rules, which also concern state-owned companies or companies with strong governmental influences."