The FAA had issued special precautions for installation of such batteries on board the 787s.
Francesco Ciucci, a mechanical engineering professor at Hong Kong University of Science and Technology who studies fuel cells and batteries, said that lithium ion batteries pose safety hazards but the risks can be minimized with safety systems that would not add much to an airplane's weight or complexity.
Ciucci said that lithium-ion batteries have been known to break down due to "thermal mismanagement," in other words, letting the temperature rise too much, which could cause batteries to swell.
"I'm very, very surprised because some of these issues, such as thermal and electrical management, have been essentially covered by various companies, in various capacities, so I'm thinking that perhaps it's just a single incident or an engineering glitch," he said.
Boeing said it was working around the clock with investigators.
"We are confident the 787 is safe, and we stand behind its overall integrity," Jim McNerney, company chairman, president and CEO said in a statement.
Japan's transport ministry categorized Wednesday's problem as a "serious incident" that could have led to an accident.
The ministry had already started a separate inspection Monday of a 787 operated by Japan Airlines that had leaked fuel in Tokyo and Boston, where the flight originated.
In a Jan. 7 incident, a fire ignited in the battery pack of an auxiliary power unit of an empty Japan Airlines 787 on the tarmac in Boston. It took firefighters 40 minutes to put out the blaze.
A computer problem, a minor fuel leak and a cracked windscreen in a cockpit were also reported on a 787 in Japan this month.
Boeing has said that various technical problems are to be expected in the early days of any aircraft model.
Much remains uncertain about the problems being experienced by the 787, said Masaharu Hirokane, analyst at Nomura Securities Co. in Tokyo.
"You need to ensure safety 100 percent, and then you also have to get people to feel that the jet is 100 percent safe," Hirokane said.
AP Business Writer Kelvin Chan in Hong Kong and Associated Press writers Joan Lowy in Washington and Mari Yamaguchi in Tokyo contributed to this report.