"Kairos was launched... but the rocket terminated its flight after judging that the achievement of its mission would be difficult," Space One said in a statement, adding that the details were under investigation.
Television footage showed the slim, white rocket blasting off and soaring far into the sky from the company's coastal Spaceport Kii launch pad in the western Wakayama region.
It was later seen spiralling downwards in the distance.
No dramatic explosion was captured by the TV cameras -- unlike at the first launch attempt in March, when the rocket blew up in mid-air just seconds after taking off.
The solid-fuel rocket had been carrying five satellites, including one from the Taiwan Space Agency and others designed by Japanese students and corporate ventures.
Space One wants to establish a satellite-launching service to tap into rapidly expanding global demand.
Private companies say they can offer cheaper and more frequent space exploration opportunities than governments, and Space One hopes to emulate Elon Musk's SpaceX, which has contracts with NASA and the Pentagon.
But first, it needs to get off the ground.
In March, the 18-metre (60-foot) Kairos, then carrying a small government test satellite, was ordered to self-destruct due to technical problems, causing the rocket to erupt in flames.
Space One was founded in 2018 by businesses including Canon Electronics, IHI Aerospace, construction firm Shimizu, and the government-run Development Bank of Japan.
The Japan Aerospace Exploration Agency (JAXA) is also on a mission to become a major player for satellite launches.
JAXA's next-generation H3 launch system had experienced multiple failed take-off attempts before a successful blast-off in February.
Also this year, Japan landed an unmanned probe on the Moon -- albeit at a crooked angle -- making it just the fifth country to achieve a soft landing on the lunar surface.
But JAXA had to delay the launch of a compact, solid-fuel Epsilon S rocket after a recent engine test resulted in a large fire.
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