A company spokeswoman said discolouring on an electrical panel had been caused by vibrations from an insufficiently tightened nut during the flight on May 4, but added the incident was not connected to previous battery problems.
"The problem occurred in one particular airplane alone, and we have already fixed the trouble," the spokeswoman said. "We believe the incident will not affect the safety of 787 flights."
The incident, which ANA characterised as "minor", is the first fault to be reported since regulators gave the green light to Boeing to get its next-generation aircraft back in the skies after a months-long hiatus.
Dreamliners worldwide were grounded after two separate incidents on Japanese-owned planes involving overheating in the lithium-ion battery packs in January.
ANA said there had been no risk to the plane and it had landed normally after what it said was a "training flight" from Tokyo's Haneda airport to Chitose in the northern island of Hokkaido on May 4.
The airline, the single biggest customer of the lightweight plane, which operates around a third of the 50 that Boeing has delivered, said the glitch would not affect the resumption of flights planned for June.