The 787 Dreamliner has suffered more than a week of bad news that has prompted investigations by aviation regulators in Japan and the United States, Boeing's home market, although the US manufacturer insists the plane is safe.
"It is true that the aircraft has recently seen a series of troubles," ANA spokeswoman Naoko Yamamoto said. "But we cannot say if this has something in common with previous problems."
ANA said 129 passengers and eight crew were on board the flight, which was headed from Ube in Japan's far west to Tokyo.
Television pictures showed emergency chutes deployed from the plane after it was forced to make the emergency landing at an airport in Takamatsu, on Japan's fourth largest island of Shikoku.
Jiji Press -- which reported smoke had been seen inside the cockpit -- and broadcaster NHK said nobody on board was injured.
"It made an emergency landing at Takamatsu because there was an error message during the flight," Yamamoto said.
Another ANA official said: "During the flight (the pilots) had an error message saying 'battery problem'. We are still investigating what exactly happened," he added, without confirming the reports of smoke in the cockpit.
Boeing said it was aware of the incident in Takamatsu. "We will be working with our customers and the appropriate regulatory agencies," the company said in a statement.
The high-profile incidents over the past week are the latest issues to dog the aircraft, after production glitches delayed delivery of the first plane to ANA by three years.
ANA and rival Japan Airlines (JAL) are among Boeing's most important clients for the Dreamliner, with a combined 100-plus planes either already delivered or on order, in deals worth billions of dollars.
Problems bloomed last week with a fire that sent smoke into the cabin of an empty JAL flight after it landed in Boston.
The airline said the smoke was traced to a fire from the battery used for the plane's auxiliary power unit, located in an electrical room at the rear of the plane.
That incident was followed by a fuel leak, also in Boston.
A cracked cockpit window forced the cancellation of another flight in Japan before a JAL-operated plane suffered a fuel spill on Sunday at Tokyo's Narita Airport.
On Friday US regulators announced an in-depth safety review of the 787, which was followed on Monday by the announcement of a probe in Japan. But Boeing insists that it has "complete confidence" in the plane.
Considered a milestone in the aviation industry with its use of lightweight composite materials and electronics instead of aluminium and hydraulics, 50 of the US aerospace giant's 787s are in service worldwide.
But questions about its safety, and the US and Japanese government reviews, have the potential to impact Boeing sales. The US aerospace giant has more than 800 787s on order.