Defense Minister Gen Nakatani issued the order after reports of suspicious activity at Pyongyang's main satellite complex, media reports said on Friday.
"Increased activity at North Korea's missile site suggests that there may be a launch in the next few weeks," Reuters quoted a source with direct knowledge of the order as saying.
Nakatani has reportedly ordered Aegis destroyers in the Sea of Japan to be ready to target any North Korean projectiles heading for Japan.
Rising tensions follow North Korea's fourth nuclear test earlier this month of what it said was a hydrogen bomb.
"A missile test coming so soon after the nuclear test would raise concern that North Korea plans to fit nuclear warheads on its missiles, giving it the capability to launch a strike," Reuters said.
Japanese Foreign Minister Fumio Kishida held telephone talks with US Secretary of State John Kerry, with whom he “exchanged information on how to cooperate from now on.”
“We can’t deny the possibility that North Korea will take further provocative action,” Kishida told reporters in Tokyo.
Pyongyang last conducted a long-range rocket launch in late 2012, successfully putting a satellite into orbit.
At the time, the West said the launch was part of Pyongyang’s efforts to build an intercontinental ballistic missile. The North, however, insists that it was a purely scientific operation.
North Korea accuses the US of plotting with regional allies to topple its government.
Pyongyang says it will not relinquish its nuclear deterrence unless the US ends its hostile policy toward North Korea and dissolves the US-led military command in South Korea.
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