The fine comes as the European Commission is poised to complete an anti-trust probe targeting Gazprom over concerns the Russian energy giant was hindering competition across central and eastern Europe.
Lithuanian competition authorities imposed their fine after finding that Gazprom had illegally blocked the country's Lietuvos Energijos Gamyba electrical utility from concluding a swap deal with another supplier for cheaper gas in 2013-2015.
The move "led to negative consequences for Lithuanian electricity and heat consumers," the authority said in a statement on Tuesday.
The country of three million still imports all of its natural gas from Russia.
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Taking control of the infrastructure is key to its energy diversification strategy, which is focused on a liquefied natural gas (LNG) terminal due to open on its Baltic Sea coast by the end of this year.
Earlier this month Lithuania's gas utility said it had reached an agreement with Gazprom to slash the price of its natural gas deliveries to Lithuania.