Boeing said the problem on a Japan Airlines 787 yesterday was discovered during scheduled maintenance and no passengers were on board. The company said it appeared that a single battery cell "vented", or released gas.
Japan Airlines said a mechanic briefly saw white smoke rise from the area below the cockpit but there was no sign it burned.
The battery has been removed from the aircraft for further investigation at its maker, GS Yuasa. JAL spokesman Kentaro Nakamura said the cause was being investigated and may take some time. Boeing experts were expected to join the Japanese probe.
He said the latest incident was unfortunate but "it demonstrated that the safety measures taken last year have actually functioned".
Mr Nakamura said JAL had no immediate plans to ground other 787s.
The incident comes a year after a fire in a lithium ion battery aboard a Japan Airlines 787 parked at Boston's Logan International Airport. That was followed nine days later by another battery incident that forced an emergency landing in Japan by an All Nippon Airways 787.
Those problems prompted the FAA and other authorities to ground all 787s for more than three months. The planes began flying again after Boeing changed the battery system, adding a tougher box to hold the battery and measures to contain any short-circuit or fire.
Boeing said those changes appeared to have worked as designed in the battery incident yesterday. It said it was working with Japan Airlines to get the plane flying again.
Because the incident happened in Japan and involved a Japanese airline, the country's authorities will lead any investigation.
If the Japan Transport Safety Board opens an investigation, the US National Transportation Safety Board "would certainly participate", NTSB spokesman Peter Knudson said. The NTSB said the incident was reported to it as a "smoke event".
The NTSB expects to finish its investigation of the 787 fire in Boston by the end of March, and present findings at a public meeting this autumn.
"Anything we can learn about the (latest) battery failure would be helpful" to the investigation, Mr Knudson said.
The Federal Aviation Administration said it was working with Boeing and with the Civil Aviation Bureau of Japan to investigate the latest malfunction.
United Airlines is the only US 787 operator and spokeswoman Christen David said: "Our 787s are operating normally, and we haven't experienced any issues with the batteries."