In a breach the defence ministry hurried to fix, Flightradar 24, a website and mobile app that enables users to track air traffic around the world, had been carrying details of Shinzo Abe's official flights as he travelled abroad.
The defence ministry, which is in charge of the official planes, does not normally disclose details of such flights for security concerns.
But Japan's biggest-selling daily, the Yomiuri Shimbun, noted the realtime coordinates and altitude of Japanese Air Force One and Two — the two planes always fly together — were available online.
"The ministry asked the company to make the change on August 8 and confirmed the firm took action on August 27," a ministry spokesman told AFP.
"We don't consider it would have seriously affected the safety of official flights, but it was not preferable that undisclosed information was made openly available to the public," he added.
Using Flightradar 24, which processes data sent from aircraft, anyone on a smartphone or computer was able to see where Japan's official planes, which carry the premier as well as the emperor and empress, was going.
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