It was scheduled to fly from the Yamaguchi prefecture in western Japan to Tokyo's Haneda Airport.
But the domestic flight was grounded by Japan's ANA because brake parts to the rear left undercarriage needed replacing, a spokesman at Yamaguchi Ube Airport said.
An ANA spokeswoman said: "In the cockpit, an error message related to its brake system was displayed.
"The exact nature and the cause of the error message is not clear yet."
All 98 passengers on board were switched to another flight for Tokyo.
On Tuesday, a Japan Airlines jet was grounded at Boston Logan International Airport in the US following a fuel leak, a day after another plane of the same type suffered a fire.
About 40 gallons (150 litres) of fuel spilled from the jet that was supposed to be bound for Tokyo from Boston last night.
Massachusetts Port Authority spokesman Richard Walsh said the plane had 178 passengers and 11 crew members on board.
The plane was evaluated and departed the same afternoon. JAL said the crew had reported a "mechanical issue."
On Monday, a fire broke out in a battery pack in the belly of a different Boeing 787 operated by JAL at the same airport.
Just minutes after all 173 passengers and 11 crew disembarked, the aircraft's cabin and cockpit filled with smoke.
It had just landed at Boston, following a non-stop flight from Tokyo.
The blaze, which was extinguished within 20 minutes, is being investigated by US aviation officials.
All three episodes have heightened safety concerns about the aircraft, which has been beset with problems.
Electrical faults have affected flights and delayed deliveries of the new jet to operators.
US manufacturer Boeing has sold 848 of the planes.
The latest episode comes after the Federal Aviation Administration - the US aviation watchdog - had already launched a probe and discovered fuel line assembly errors.
It said that the faults could result in fire risk from leaks dripping on hot engine parts or causing the aircraft to run out of fuel.
Japan Airlines said it had no plans to change placed orders of 38 Boeing 787 Dreamliners following the two incidents.
The company has ordered 45 in total, seven of which it is already operating. A spokesman said six were currently in use, the other at Boston Logan International Airport.
All Nippon Airways, which has placed orders for 66 Dreamliner aircraft, including 17 already in use, also said it had no plans to change its orders.
British Airways has ordered 24 Dreamliners from Boeing and is still expecting its first 787 in May, with a further three due for delivery before the end of 2013.
Virgin Atlantic has 16 jets on order and told Sky News it still expects its first delivery in 2014.
Thomson Airways has also placed orders for the hi-tech long-haul Boeing plane, which has been marketed as being more comfortable and environmentally friendly than other aircraft.
A spokeswoman for Thomson told Sky News: "Our first Thomson Dreamliner is still on track to be delivered early this year. Boeing has reassured us that they are taking action to rectify the issues highlighted to them."
State-owned Air India, on Monday took delivery of the sixth of the 27 Dreamliners it has ordered said precuationary measures were already in place and its planes were flying smoothly.
"It's a new plane, and some minor glitches do happen. It's not a cause of concern," said spokesman G Prasada Rao.
Air China and Hainan Airlines also said they would be keeping their orders for 15 and 10 of the planes.
Qatar Airways chief executive Akbar al Baker, who previously criticised Boeing after its delivery-delayed planes were grounded for five days because of electrical faults, said there were no technical problems with the five currently in use by the Gulf carrier.
Other carriers already flying the Dreamliner are Ethiopian Airlines, LAN Airlines, LOT Polish Airlines and United Airlines.
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