The launch was halted just before the rocket's scheduled liftoff at 11.11am from the Tanegashima Space Centre in Kagoshima Prefecture, southwestern Japan.
A system to inject cooling water at the launch pad automatically stopped 16.8 seconds before liftoff after a sensor detected insufficient water levels, JAXA said.
When launching a large rocket, a significant amount of water is poured onto a firewall and a smoke path under the launch pad to prevent damage from high heat and vibrations caused by the firing engine.
The rocket was to carry a Michibiki satellite, which will be part of the Japanese version of GPS.
"We apologise to everyone who was eagerly waiting for the launch," Makoto Arita, JAXA's H3 project manager, told a press conference. "We hope to resume the launch as soon as possible," he added.
JAXA has yet to decide on a new launch date.
Japan plans to use seven Michibiki satellites to enable round-the-clock location monitoring that does not rely on data from other countries by the end of this fiscal year.
The launch of a seventh Michibiki satellite is scheduled for February next year.
The maiden launch of the H3 rocket, developed by JAXA and Mitsubishi Heavy Industries Ltd., failed in March 2023.
It had since achieved five consecutive successful launches.
[Copyright The Jiji Press, Ltd.]