While the error is not uncommon among other plane models it is the latest glitch for the once-grounded high-tech plane after a run of more serious setbacks.
Flight 641, a Boeing 787 operated by All Nippon Airways (ANA), left Tokyo’s Haneda airport at 9am (0000 GMT) for the southern Japanese city of Kumamoto, carrying 234 passengers and nine crew members.
But the plane returned to Haneda by 10:20am due to “trouble with the weather radar”, ANA spokesman Ryosei Nomura told AFP.
All passengers got on another 787 at Haneda and safely arrived in Kumamoto early afternoon, he said.
Nomura said this kind of trouble “could happen in other models of airplane”.
“It wasn’t an irregularity peculiar to the 787,” he said.
The 787 faced a global grounding order in January after lithium-ion batteries overheated on two different planes, with one of them catching fire while the aircraft was parked.
Japan Airlines and ANA, the single biggest operator of 787s, put their full fleets of Dreamliners back into service following a four-month suspension.