The European Commission said last week that it was concerned that Gazprom abused its market position in the upstream natural gas sector in Central and Eastern Europe.
Putin said on the sidelines of a summit for the Asia-Pacific Economic Cooperation that European leaders were playing politics with the energy issue.
"Europe wants to maintain political influence (in the region) but in such a way that we pay for it a little," he was quoted by Russia's state-run news agency RIA Novosti as saying.
The European Commission said it would examine whether Gazprom was interfering with competition in the regional gas market. Gazprom, the commission said, may have divided gas markets by hindering the free flow of gas across European member states.
Putin described the investigation as counterproductive but cautioned it didn't amount to a trade war with Europe.
"I hope the situation will be resolved without any problems for either Gazprom or the EU," he said.