Japan and Russia have never signed a treaty to mark the end of World War II because of a territorial dispute but they are moving to deepen ties despite that, and despite Russian concern about Japan's role in a US missile defense programme.
The foreign ministers of both countries said the meeting helped build trust.
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"This would also have a positive impact on the negotiations to sign a peace treaty."
Japan and Russia both claim remote, windswept islets called the Northern Territories in Japan and the Southern Kuriles in Russia.
Japanese Prime Minister Shinzo Abe and Russian President Vladimir Putin, who have met four times in the last six months, agreed in April to revive talks on resolving the dispute and a vice ministerial-level meeting will be held next year.
On Saturday, the two sides agreed to hold naval exercises to combat terrorism and piracy and to deepen their cooperation in regional security and diplomatic forums.
Russia invited the Japanese ministers to Moscow in 2014 for more talks, Russian Foreign Minister Sergei Lavrov said.
Neither side referred explicitly to worries about China's rising power and Kishida said security cooperation between Japan and Russia was not being undertaken with any other country in mind.
The path to a good relations between Japan and Russia may not be entirely smooth.
Russia expressed concern over Japan's moves to strengthen its defense alliance with the United States including a plan to locate a US missile-defense radar system in Japan.
"We openly communicated that we are concerned about Japan's participation in the United States' global missile defense system," Russian Defence Minister Sergei Shoigu said.
Relations between Russia and the United States have been strained by disputes over Iran, Syria, and Russia's decision to give temporary asylum to US fugitive spy contractor Edward Snowden.
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