Japan's All Nippon Airways on Friday said a modified Dreamliner had experienced a fault earlier this month, but insisted it would not affect the restart of the high-tech planes.
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 issues.
"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, one of which provoked a fire on a parked plane in Boston.
After months of investigations into the plane's powerpacks, US authorities last month issued formal approval of Boeing's battery fix, followed by a similar move from Japanese regulators.
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.
ANA began testing its Dreamliner fleet at the end of April, with a two-hour flight from Haneda Airport that had ANA chairman Shinichiro Ito and Boeing Commercial Airplanes CEO Ray Conner aboard as part of a push to reassure Japan's consumers the plane was safe.
"After three months it's a terrific feeling to have an ANA 787 back in the air, and I am very pleased to say that it was a perfect flight on a perfect day," Conner told reporters at the time.
"As is evident by the fact that we are here today, we are very confident in the solution that we developed... and I can tell you that we put our family on this airplane on any day of a week, and any time."
ANA and Boeing have been anxious to put the damaging crisis behind them and have been looking to turn the page.
The airline subsequently announced it would resume use of the Dreamliner on international and domestic routes, including those linking Tokyo's Narita airport to San Jose, California, and between Haneda and Frankfurt.
The plane's manufacturer said Tuesday it had resumed deliveries, with ANA the first company to get the keys to a new jet, which arrived in Japan on Thursday evening.
"Despite the disruption in deliveries over the past several months, we still expect to deliver all the 787s we originally planned to by the end of the year," Randy Tinseth, Boeing vice president of marketing for Boeing Commercial Airplanes, said in a Boeing blog.
"We once again thank our customers for their patience and confidence as we begin delivering on our commitments."
Tokyo-listed shares in ANA were down two yen at 218 by lunchtime.