Russian Foreign Minister Sergey Lavrov and his Japanese counterpart, Fumio Kishida, also joined in urging North Korea to refrain from "provocative actions" and to abide by United Nations resolutions demanding an end to its nuclear and missile testing.
The call came in "two-plus-two" talks among foreign and defense ministers in Tokyo that touched on a wide array of issues, including the conflict in Syria, drug trafficking, and logistics for travel by elderly Japanese back to disputed islands that have been under Russian control since the end of World War II.
The meetings in Tokyo were the two countries' first "two-plus-two" talks since Russia's annexation of Crimea from Ukraine.
Japanese Prime Minister Shinzo Abe is to visit Russia in late April and again in September, as the two sides haggle over how to narrow differences in the territorial dispute that has prevented them from reaching a peace treaty officially ending their World War II hostilities.
But while the talks appeared cordial and the tone was constructive, tensions remain.
Earlier this month, North Korea fired four missiles, of which three landed inside Japan's territorial waters. Russia views missile defense systems the U.S., Japan's main ally, is deploying in northeast Asia as a threat to regional security, Lavrov said following the talks.
The US and South Korea have agreed to install an advanced anti-missile system as a defense against North Korea. The Terminal High-Altitude Area Defense system, or THAAD, has angered both Russia and China. Russia also objects to U.S. missile defense systems in Japan.
"The U.S. Global ballistic missile defense poses a deep risk to the security of the region," Lavrov said. He said it was crucial to avoid upsetting the balance in the region and setting off an even greater arms buildup that could lead North Korea to step up its own military expansion.
Lavrov said the installation of the THAAD system was "a response completely out of proportion" to the threat from North Korea. He accused the U.S. Of "pumping arms into the region," and called for approaches that might encourage North Korea to engage in dialogue with its neighbors.
Lavrov met with Japanese Foreign Minister Fumio Kishida, and Russian Defense Minister Sergei Shoigu held talks with his Japanese counterpart, Tomomi Inada. The four ministers then held combined talks on international and bilateral issues. "Based on the talks today, we hope to firmly work toward developing Japan-Russian cooperation in various areas," Kishida said afterward.