McNerney did not mention specifics about the recent incidents, but said the company "deeply regrets the impact that recent events have had on the operating schedules of our customers and the inconvenience to them and their passengers."
The batteries are critical to the plane because the 787 is thirsty for electrical power.
The Dreamliner uses electricity to run more systems than any other Boeing airliner, said University of Dayton professor Raul Ordonez, an aircraft electrical and computer engineer who spent time observing Dreamliner development at Boeing's Seattle headquarters.
The 787 is unique because its batteries are lithium-ion batteries. These hold more energy for longer periods than the standard nickel cadmium airliner batteries.
"These kinds of batteries," Ordonez says, "are slightly more likely to cause problems."
Although lithium batteries heat up quickly because of their structure, they have systems and circuits in place to prevent overheating, said Tsutomu Nishijima, a spokesman for GS Yuasa.
The Japanese company supplies batteries for Dreamliners.
Investigation expected to take weeks
The investigation will take several weeks, the company said.
Boeing has delivered 50 Dreamliners so far and has more than 800 additional orders from airlines around the world.
Carriers who have ordered planes but are still awaiting delivery, like Qantas of Australia and Etihad in the United Arab Emirates, expressed confidence that the problems would be sorted out by the time they received the planes.
Boeing's shares, which had previously been resilient in the face of this month's negative publicity over the Dreamliner, sank another 2% on Thursday.
After last week's incident in Boston, Boeing chief engineer Mike Sinnett expressed confidence in the aircraft's battery system.
"I am 100% convinced the airplane is safe to fly," he said. "I fly on it all the time."
Longtime commercial pilot and industry analyst Patrick Smith said the battery issue did not appear to be a major problem, but called the FAA order "a positive and pro-active step."
"I don't think that it was dangerous for the plane to be flying, but it probably wasn't the best thing to be flying it on the heels of this latest emergency landing in Japan," Smith said.
"All airplanes have their teething problems, and this was trending in a bad direction," he added. "Now the authorities have said, 'Stop,' and that's a good thing."