"We have touched upon the issues that concern Japan and Russia, first of all in terms of security, and agreed that we will decrease [the number of] issues where there is lack of understanding, work on aligning our positions and thus increase mutual trust," Patrushev told reporters.
When asked whether the two discussed a peace treaty between Russia and Japan, Patrushev said, "the treaty must be agreed."
"We have to create conditions for that, this is what we will be doing," he said.
Patrushev met in Tokyo with Japanese Prime Minister Shinzo Abe to discuss bilateral cooperation as well as international and regional security.
"The Japanese prime minister received the Russian security council secretary in Tokyo. Nikolai Patrushev and Shinzo Abe discussed a wide range of issues of Russian-Japanese cooperation in various fields, as well as issues of international and regional security," the Russian Security Council said in a statement.
Moscow and Tokyo have not signed a permanent peace treaty after the end of World War II. The dispute over the southern Kuril Islands has been one of the main stumbling blocks in the peace talks.
In 1956, both sides signed a joint declaration that provided for the restoration of bilateral relations after the end of World War II. The Soviet Union also agreed to consider handing over two out four disputed islands — Habomai and Shikotan — to Japan, but Tokyo insisted on getting all the Southern Kurils, referring to them as "Northern Territories".