It is the latest in a series of incidents to heighten safety concerns over the plane.
All Nippon Airways (ANA) said instruments aboard a domestic flight indicated a battery error, triggering emergency warnings to the pilots. The Civil Aviation Bureau said a second warning light indicated smoke.
The incident, described by officials as "highly serious" – language used in international safety circles as indicating there could have been an accident – is the latest in a line of mishaps, including fuel leaks, a battery fire, wiring problem, brake computer glitch and cracked cockpit window, to hit the airliner in recent days. ANA grounded all 17 of its 787s, and Japan Airlines suspended its 787 flights.
ANA flight 692 left Yamaguchi in western Japan shortly after 11pm GMT on Tuesday bound for Haneda Airport near Tokyo. About 18 minutes in, the plane descended and made an emergency landing 16 minutes later.
Authorities said the plane landed at Takamatsu. All 129 passengers and eight crew evacuated via inflatable chutes. Five people were slightly injured.
A Boeing spokesman said: "We're aware of the events and are working with our customer."