The order from Defense Minister Naoki Tanaka came at a meeting of Japan's national security council. It followed instructions issued earlier in the week for the military to prepare to intercept the satellite rocket if it enters Japanese territory.
The Unha-3 rocket is expected to fly past western Japan after its launch from North Korea's west coast sometime between April 14 and 16. The plan has raised concerns that a failed launch, or a falling stage of the rocket, could endanger Japanese lives or property.
A statement from the Defense Ministry said Japan would send destroyers equipped with Aegis missile defense systems to the Pacific and East China Sea and deploy mobile Patriot missile launchers to islands in Okinawa. An interceptor missile unit is also likely to be deployed in Tokyo, although the capital is well away from the expected flight path.
Seoul has also warned it might shoot down any parts of the North Korean rocket that pass over South Korean territory.
North Korea has said it plans to launch a satellite into orbit. Japan, the United States and other countries claim it is also seeking to test the capabilities of its long-range missiles, in violation of international agreements.
Japan mobilized its interceptor units and issued a similar warning to North Korea before a rocket launch in 2009, but did not follow through.
Interceptor missiles on the Japanese destroyers would serve as the first line of defense, and the land-based Patriot missiles would be a backup. Japan has successfully tested its interceptor missiles, but has never used them in a real-world situation.