A government official confirmed that an order was issued. The official declined to be identified as he is not authorised to speak to the media.
The order was first reported by state broadcaster NHK. A spokesman for the Ministry of Defence earlier declined to comment, as did South Korea's defence ministry.
Japan has put its anti-ballistic missile forces on alert at least twice this year after detecting signs of launches by North Korea.
North Korea conducted its fourth nuclear test in January and has followed that with test launches of various missiles.
Japan has advanced Aegis vessels in the Sea of Japan that are able to track multiple targets and are armed with SM-3 missiles designed to destroy incoming warheads in space before they re-enter the atmosphere and fall to there targets.
Patriot PAC-3 missile batteries, designed to hit warheads near the ground, are deployed around Tokyo and other sites as a second and final line of defence.