Sergei Shoigu said the system is of "grave concern" to Russia because of "the possible destruction of the strategic balance of power in the Asia-Pacific region," RIA Novosti reported.
Japanese Foreign Minister Fumio Kishida told the conference "the linchpin of Japan's defense policy remains its union with the U.S., and there will be no changes in this respect."
The meeting between the countries was the first in the so-called "2+2" format, in which foreign and defense ministers meet together.
Despite disagreement over the missile system, Japanese Defense Minister Itsumori Onodera said the talks produced agreement on both sides to hold joint military exercises to counter terrorism and piracy.
Shoigu said Japan and Russia had proposed increasing coordination of Russian and Japanese naval vessels in the Horn of Africa, where piracy is prevalent.
Kishida said increasing cooperation between Russia and Japan was important "for fortifying peace and stability" in the Pacific Ocean region.
The countries will start holding meetings on cybersecurity, the Japanese foreign minister said.