Japan's government has admitted that the flight paths of official aircraft used by Prime Minister Shinzo Abe were posted online.
The location of the planes and other flight data were published on the website Flightradar24, which shows live air traffic around the world, local reports said.
The defence ministry said it had asked the website to remove the information.
Officials said they had confirmed the data was removed on 27 August.
"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," a defence ministry official told AFP news agency.
The two Boeing 747-400 planes, dubbed Japan's Air Force One and Air Force Two, always travel together, according to AFP. They also transport the imperial family.
Flightradar24 says it tracks flights primarily through signals which are broadcast by aircraft, called ADS-B. It also uses data provided by the US Federal Aviation Administration and a navigation technique called multilateration.
The site relies on a network of 4,000 data receivers, hosted by volunteers around the world, which send the information to its servers.
Japan announced earlier this month that it would replace the two aircraft with Boeing 777-300ERs, which will be operational from April 2019.
The new planes have the ability to fly nonstop to the US east coast and are large enough for VIPs, their entourages and communication equipment to handle sensitive information, reported Mainichi.