The plan is detailed in Japan's annual white paper on national defense, which should be adopted by the end of 2010, RIA Novosti reported.
The missiles are deployed at three air bases in Japan, but additional systems will be placed on all major Japanese islands, the document said.
North Korea became one of Japan's biggest security concerns after it test-fired a long-range ballistic missile over Japan in 1998.
The concern grew after North Korea conducted a series of ballistic missile tests in July 2006, followed by an underground nuclear test three months later, the report said.
Japan is one of a dozen countries to choose the combat-proven Patriot missile system as a major component of their air and missile defense programs.
North Korea's medium-range ballistic missiles have a range of more than 800 miles.