Japan's two biggest airlines, the US aviation agency, and Air India took action after the incident yesterday.
The 787, known as the Dreamliner, is Boeing's newest jet, and the company is counting heavily on its success.
But since its launch after delays of more than three years, the plane has been plagued by a series of problems including a battery fire and fuel leaks.
The 787 that landed yesterday had been leaking electrolyte and burn marks were found around the main battery, located in an electrical room below the cockpit, according to All Nippon Airways (ANA).
The domestic flight landed at Takamatsu airport in western Japan after a cockpit message showed battery problems and a burning smell was detected in the cockpit and cabin.
Japan's ANA and Japan Airlines are major customers for the jet and among the first to fly it.
Japan's transport ministry said it received notices from ANA, which operates 17 of the jets, and Japan Airlines, which has seven, that all their 787s would not be flying.
In Washington, the Federal Aviation Administration (FAA) was temporarily requiring US carriers to stop flying 787s.
United Airlines has six of the jets and is the only US carrier flying the model, but aviation authorities in other countries usually follow the lead of the country where the manufacturer is based.
ANA executives apologised, bowing deeply at a hastily called news conference in Tokyo.
"We are very sorry to have caused passengers and their family members so much concern," said senior executive vice president Osamu Shinobe.
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 categorised yesterday's problem as a "serious incident" that could have led to an accident, and sent officials for further checks to Takamatsu airport.
Boeing, the US National Transportation Safety Board and the FAA were sending representatives to work with the Japanese government on the investigation, NTSB spokeswoman Kelly Nantel said.
It was unclear how long the Dreamliners would be grounded. ANA and JAL cancelled some flights or switched aircraft.
Video shot by a Japanese TV reporter on board the ANA flight showed the interior of the plane as passengers were evacuating, sliding down chutes, and then walking away on the tarmac.
ANA and the fire department said one man had minor hip injuries from using the emergency slide, but the other 128 passengers and eight crew members were uninjured.
Japan's transport ministry had already started a separate inspection on Monday of a 787 operated by Japan Airlines that had leaked fuel in Tokyo and Boston, where the flight originated.
Boeing has said that various technical problems are to be expected in the early days of any aircraft model.
The 787 relies more than any other modern airliner on electrical signals to help power nearly everything the plane does.
Air India said it has grounded its fleet of six Boeing 787 aircraft under orders from Indian aviation authorities.
Its spokesman said they today directed the state airline to stop flying the Boeing planes until an investigation by Indian regulatory authorities takes place.
"Air India has temporary ceased operation of its Dreamliners," he said.