The new Army Navy/Transportable Radar Surveillance system (AN/TPY-2) aims to "enhance sensor coverage for ballistic missile defense of Japan and the US homeland," the Defense Department said in a statement.
The United States has said it wanted its allies to enhance their missile defenses to help protect against a belligerent North Korea.
North Korea's nuclear and ballistic missile program is a major security concern in the Pacific region and beyond.
"We will continue to emphasize the importance of developing regional ballistic missile defense systems," Joints Chief of Staff vice-chairman James Winnefeld said earlier this year, emphasizing that cooperation would "result in better performance than individual countries acting alone."
Dubbed the Kyogamisaki Communications Site, the new radar will be located in Kyogamisaki, some 375 miles (600 kilometers) west of Tokyo. The existing radar system is in Shariki, in northern Japan.
The facility was tested and constructed in Japan by the US military in cooperation with Japan, the Pentagon said.