The two countries have diplomatic relations but ties have been strained by a dispute over four islands, known in Japan as the Northern Territories and in Russia as part of the Kuril Islands.
Chikahito Harada, Japan's special envoy for Japan-Russia relations, and Russian Deputy Foreign Minister Igor Morgulov met in Tokyo for the one-day meeting.
"We're going to tackle this issue in a new way to break the deadlock that has lasted until now," Harada said, according to Jiji Press news agency.
The former Soviet Union declared war on Japan in the closing days of the conflict in 1945, attacking Tokyo's puppet state of Manchukuo in northeastern China and seizing Japanese islands north of Hokkaido.
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Hundreds of thousands of Japanese soldiers were taken prisoner and moved to Siberia where they were forced to labour for about a decade before those who survived were allowed to return home.
Today's talks marked the first negotiation between Japan and Russia since Prime Minister Shinzo Abe and President Vladimir Putin met in Sochi in May to discuss the dispute.
Abe, during the meeting -- a rare visit to Russia by a Group of Seven leader -- agreed with Putin to push the negotiations forward by employing "a new approach without being bothered by the old previous thinking".
Putin is expected to visit Japan later this year.
Over the years leaders from both countries have met several times to discuss the dispute but a resolution has proved elusive.
Russian Prime Minister Dmitry Medvedev visited the disputed islands -- home to some 19,000 Russians -- last year, infuriating Tokyo.