The talks were set in the hopes of restarting a dialogue over four islands that each country has claimed a right to since the end of World War II, and included a number of economic deals, 23 of which were centered on energy.
Russia has gradually been shifting its focus east following the implementation of sanctions against the country by the West over its annexation of Crimea. Prior to this weekend's deals, the focus had been on China and India, with ties between Russia and Japan complicated by the territorial dispute over the islands, which Russia refers to as the Kuril Islands, and Japan calls the Northern Territories.
Energy deals have presented an avenue for the two countries to increase cooperation, however, even as the ownership of the islands remains in contention.
"Energy is a strategic area of Russia-Japan cooperation," Putin said, noting Russia's "reliable" LNG supplies, in excess of 8 percent of Japan's needs.
Japan is also one of the top buyers of Russia's ESPO and Sokol crude.