"Japanese-U.S. cooperation in missile defense is cause of concern for us. We are against the creation of a missile defense system as a means of achieving military superiority. The deployment of such a system will spur an arms race both regionally and globally," Sergei Lavrov said in an interview published on Saturday.
He said the system is part of the U.S. global missile defense shield and could be used against Russia and China.
Tokyo and Washington have intensified joint missile defense programs since North Korea's nuclear bomb and long-range missile tests last year.
Around 50,000 U.S. troops are stationed across Japan under a bilateral security arrangement.
At high-level talks in Moscow on Friday, U.S. and Russian officials failed to make progress on missile defense and arms control disputes.
The U.S. announced plans in January to deploy interceptor missiles in Poland and a radar in the Czech Republic as part of its missile shield, aimed at countering possible threats from "rogue states" such as Iran and North Korea. Moscow strongly opposes U.S. plans, considering them a threat to its national security.