The expansion of the American global missile defense system is a heated issue for Russia, which strongly opposes Washington's plans to deploy a missile shield in Central Europe.
Masahiko Komura told Sergei Lavrov in Moscow: "When Japan makes decisions, it always takes other countries' concerns and interests into account."
"As to U.S. plans to deploy missile defense elements [in Japan], this is a measure that has been forced by Japan's close location to North Korea, which has conducted a nuclear weapon test."
Lavrov said Russia accepts "Japan's explanation regarding the absence of any intention to use Japan's participation in missile defense deployment in the region together with the U.S. to the detriment of Russia's interests."
He said dialogue will be continued to clarify any problems.
"We believe the best way to monitor and, if necessary, neutralize missiles is to create a true security system uniting the U.S., European countries and all interested sides, including Japan," Lavrov said.
The diplomats reached an agreement at the talks to continue negotiations on a bilateral peace treaty to formally end World War II hostilities.
Russia and Japan have failed to sign a formal peace treaty due to their territorial dispute over the South Kuril Islands, former Japanese territory annexed by the Soviet Union after World War II.