Tokyo-based Space One's 18-metre (60-foot) Kairos rocket blasted off in the coastal Wakayama region of western Japan, carrying a small government test satellite.
But around five seconds later, the solid-fuel rocket erupted in fire, sending white smoke billowing around the remote mountainous area as orange flames raged on the ground, live footage showed.
Space One said it had taken the decision to "abort the flight" and details were being investigated.
"We want to accept this outcome in a forward-looking manner and embark on our next challenge," company president Masakazu Toyoda told reporters, asserting that Space One does not use the term "failure".
The firm wishes to "contribute to the expansion of space-related services" through successful satellite launches by its rockets in the future, he added.
Burning debris fell onto the surrounding slopes as sprinklers began spraying water, in dramatic scenes watched by hundreds of spectators gathered at public viewing areas including a nearby waterfront.
Private companies like Space One are playing an increasingly important role in space exploration worldwide.
Last month a Houston-based company landed America's first spaceship on the Moon in more than 50 years, and rockets made by Elon Musk's SpaceX have come to be heavily relied upon by NASA.
But failures are rife, and last year another Japanese start-up, ispace, tried in vain to become the first private company to land on the Moon.
The company said it had lost communication with its craft in what it described as a "hard landing".
- 'Didn't even imagine' -
Space One is hoping to become Japan's first private firm to put a satellite into orbit.
The plan had been for Kairos -- an ancient Greek word meaning "the right moment" -- to do so around 51 minutes after take-off on Wednesday morning.
The launch had already reportedly been postponed five times due to parts shortages and other problems, most recently on Saturday.
The mayor of Kushimoto, the district in Wakayama where Space One's launch site Spaceport Kii is located, voiced his surprise and disappointment.
"I didn't even imagine an outcome like this," Katsumasa Tashima told reporters shortly after the explosion.
The area and its 15,000 residents "will continue to support Space One," he said. "We want to continue to offer our help so that the first rocket will have a successful launch."
Space One was established in 2018 by a team of major Japanese tech businesses, including Canon Electronics, IHI Aerospace, construction firm Shimizu and the government-owned Development Bank of Japan.
The failure fuelled a sell-off of their shares, with Canon Electronics ending the day down 7.45 percent.
Last July, another Japanese rocket engine, the solid-fuel Epsilon S, exploded during a test around 50 seconds after ignition.
That was one in a string of failures for the country's space agency JAXA, including launch attempts for its next-generation H3 rocket.
JAXA eventually managed a successful blast-off last month for the H3, its new flagship rocket that has been mooted as a rival to SpaceX's Falcon 9.
That followed Japan's successful landing in January of an unmanned probe on the Moon -- albeit at a wonky angle -- making it just the fifth country to achieve a "soft landing" on the lunar surface.
hih-tmo-kaf/mca
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