The major Japanese newspaper Yomiuri Shimbun reported earlier that Washington had informally sounded out Tokyo on the plan aimed at protecting US military bases and other facilities in Japan from ballistic missile attacks.
Citing Japanese and US sources, the Yomiuri said Tokyo intended to discuss the plan soon.
The US military is considering deploying the Patriot Advanced Capability 3 (PAC-3), a US army surface-to-air guided missile that is capable of intercepting such missiles as the North Korean Rodong, which has a range of about 1,300 kilometers (810 miles), the report said.
But the report was denied by the press offices of both the Foreign Ministry and the Defence Agency.
"It is not true that the US side has consulted our government on the possible early PAC-3 deployment," a foreign ministry spokeswoman said. A similar denial was made by Defence Agency press officer Midori Sasaki.
Washington is considering a plan to transport anti-ballistic missiles and radars in C-5 transport planes from the United States to Japan when an armed attack on this country is believed to be imminent, the report added.
Japan plans to deploy in the year to March 2008 an anti-missile system consisting of the seaborne Standard Missile 3 (SM3) and the land-based PAC-3.
SM-3s intercept ballistic missiles when they reach their highest point outside of the atmosphere and then PAC-3 missiles are used to finish off the missiles that have escaped SM-3 attacks.
The PAC3 is an advanced version of the PAC-2 which the air defence force is deploying at 27 anti-aircraft artillery units nationwide.
Japan has hastened to build up a missile defense system since North Korea lobbed a suspected Taepodong missile into the Pacific in 1998, shocking the region and the world.