Russian Foreign Minister Sergey Lavrov's trip came days after Japan hosted foreign ministers from the Group of Seven industrialised nations. Russia is barred from G-7 because of its annexation of Crimea in 2014. That has also shelved Russian President Vladimir Putin's Japan visit for nearly two years.
Still, Prime Minister Shinzo Abe has been pushing to make progress in the dispute over Russian-held islands, called the Northern Territories in Japan and the southern Kurils in Russia, which has kept the two countries from signing a peace treaty formally ending their World War II hostilities.
As part of the G-7, it supports the group's diplomatic isolation of Russia. At the same time, Tokyo wants good relations with Moscow to maintain dialogue and negotiate the territorial dispute.
The two sides have stepped up economic and diplomatic cooperation despite Russia's support for rebels in eastern Ukraine.
A senior lawmaker from Abe's ruling Liberal Democratic Party met in early April with Russian Trade and Industry Minister Denis Manturov and handed him Abe's letter for Putin.