Tokyo and Washington agreed on the licensed production of PAC3 in Japan in 2004.
"It was very important interceptor missiles were deployed not far from Tokyo - the center of business and political activity - to be ready for any emergency," said Kazumasa Echizen, a spokesman for the base press service.
About 50 people gathered outside the base to protest the move.
Japanese military officials said in about 10 years all of the country's densely populated areas will be covered by 16 missile-defense complexes.
Earlier this week Lt.-Gen. Henry Obering, director of the U.S. Missile Defense Agency, said a joint U.S.-Japanese exercise will be conducted later this year to intercept a dummy missile launched from a destroyer in the Sea of Japan.
Japan's Mitsubishi Heavy Industries Ltd. started production of the PAC3, a key component of the next-generation missile defense system, in 2005 under a licensing agreement with Lockheed Martin Corp. of the United States.
The Dutch Air Force also adopted PAC3 missiles, deploying the first battery at its De Peel base Friday.
The Dutch Defense Ministry said it has bought a total of 32 PAC3 missiles with mobile launchers.
A ministry spokesman said the Netherlands will now be self-sufficient in air defense and will not have to seek U.S. assistance in providing cover for peacekeeping contingents, for example, in Afghanistan.
