Regional tensions are mounting as Washington and Pyongyang ratchet up their war of words, with President Donald Trump warning Pyongyang would "truly regret" any hostile action against the US.
The defence ministry started deploying the Patriot Advanced Capability-3 (PAC-3) system in Shimane, Hiroshima and Kochi in western Japan, which Pyongyang warned could be along its missiles' flight path, public broadcaster NHK said.
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Television footage showed military vehicles carrying launchers and other equipment for the surface-to-air system entering a Japanese base in Kochi before dawn.
While immediate confirmation of the reports was not available, Japan has in the past vowed to shoot down North Korean missiles or rockets that threaten to hit its territory.
The government hopes to complete deployment of the system in western Japan by Saturday morning, Kyodo News said, quoting defence ministry officials.
Yoshihide Suga, Japan's chief government spokesman, said earlier this week that Tokyo "can never tolerate" provocations from North Korea and the country's military, will "take necessary measures."
In 2009, a North Korean rocket passed over Japanese territory without incident or any attempt to shoot it down.
At the time North Korea said it was launching a telecommunications satellite, but Washington, Seoul and Tokyo believed Pyongyang was testing an intercontinental ballistic missile.
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