Japanese Defense Minister Itsunori Onodera issued the order, but did not make it public in order to avoid putting a chill on renewed talks between Tokyo and Pyongyang, the first in more than a year, local media reported earlier.
"The defense minister made the order to prepare for any additional missile launches," the source said.
Onodera, the source said, did not deploy Patriot missile batteries that would be the last line of defense against incoming warheads.
Media reports said the North Korean-Japanese talks in Beijing broke no new ground, but ended with an agreement for further meetings.
The firing of the Rodong coincided with a meeting in The Hague between U.S. President Barack Obama and the leaders of South Korea and Japan and followed a series of short-range rocket launches.
The launch appeared to be a show of defiance by North Korea. The missile fell into the sea after flying 650km, short of a maximum range thought to be some 1,300km.
Japanese Aegis destroyers in the Sea of Japan are equipped with advanced radar equipment able to track multiple targets and carry missiles designed to take out targets at the edge of space.
By Ruchi Singh
reporter
Park Sae-jin
swatchsjp@ajunews.com