The unmanned rocket, scheduled for launch in three stages, launched several satellites into orbit on its sixth space mission.
“The missile cannot safely continue to fly because it would pose a hazard if it hit the ground,” a JAXA official said in comments broadcast by TBS television.
“So we took measures to avoid such an incident and we sent the signal (to destroy the missile),” he said, adding that information on the cause of the problem is not immediately available.
Public broadcaster NHK and other outlets said it was Japan’s first failed rocket launch since 2003.
A JAXA live broadcast of the launch from the Uchinoura Space Center in the southern Kagoshima region was interrupted and the presenters said there was a problem, without giving details.
The Epsilon solid-fuel rocket has been in use since 2013.
Smaller than the country’s previous liquid-fueled model, it succeeds the solid-fueled M-5 rocket, which was phased out in 2006 due to its high cost.
One of the rocket-carried satellites, called RAISE-3, is expected to orbit Earth for at least a year, according to a NASA post about the launch.