"As part of measures to prepare for emergencies, we will today deploy a PAC-3 unit" to a base of the nation's Ground Self-Defense Force in the southern tip of Hokkaido, Defence Minister Itsunori Onodera told reporters.
The Patriot Advanced Capability-3 system arrived at the base later on Tuesday, a local defence official told AFP.
The move came with tensions on the Korean peninsula at fever-pitch after Pyongyang carried out its sixth nuclear test and fired two missiles over Japan in the space of less than a month.
North Korea "may take further provocative actions including launching ballistic missiles that would fly over Japan again in the future", Onodera said, adding that his ministry "would take appropriate measures to protect people's safety".
According to local officials, Japan has already deployed the PAC-3 system to another part of Hokkaido.
But defence officials declined to confirm where in Japan other systems were deployed, citing the sensitive nature of defence information.
North Korea has threatened to "sink" Japan into the sea and said Saturday it sought military "equilibrium" with arch-enemy the United States by developing a full nuclear arsenal.
Hawkish Japanese Prime Minister Shinzo Abe has said he would "never tolerate" the North's "dangerous provocative action" and has urged the international community to ramp up pressure on Pyongyang.
The UN Security Council, which condemned the launch as "highly provocative," will hold a new ministerial-level meeting Thursday on the proliferation of weapons of mass destruction, focused on enforcing sanctions on the North Korean regime.
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