"There was an abnormality during today's combustion test. We are trying to assess what happened," JAXA said.
Footage on NHK showed flames and smoke rising from the site on the southern Japanese island, DW reported.
Journalists positioned around one kilometer (0.62 miles) away reported a large explosion shortly after the test began at 8:30 a.m. local time.
Footage on national broadcaster NHK showed towering balls of fire and white fumes rising from the site.
No injuries were reported, and the cause of the incident is under investigation.
"JAXA will conduct a thorough investigation into the cause of the problem and consider countermeasures," said Chief Cabinet Secretary Yoshimasa Hayashi, the Japanese government's top spokesperson.
"The development of flagship rockets is extremely important for the independence of Japan's space development program."
But the Asahi Shimbun newspaper reported that JAXA's plan to launch the Epsilon S – the successor to the Epsilon – by March 2025 was now practically impossible.
In March a rocket made by a private Japanese company, Tokyo-based Space One, exploded seconds after launch.
SD/
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