The Federal Aviation Admistration decided late Wednesday to ground all U.S.-based Boeing 787 Dreamliner jumbo jets, after the plane's lithium ion battery caught fire in two separate incidents within a nine-day period.

As the Associated Press reports, the FAA issued an emergency directive requiring all U.S. carriers to temporarily cease operating their 787s. This comes in the wake of Japan's All Nippon Airways and Japan Airlines voluntarily grounding their fleets of the new jumbo jet. United Airlines, which operates eight 787s, is the only U.S. carrier currently using the airplane and the only one thus affected by the FAA's decision, but further groundings are likely to come, as regulatory authorities in other countries tend to follow the agency based where the airplane is manufactured.

Boeing President and CEO Jim McNerney said "we are confident the 787 is safe, and we stand behind its overall integrity" in a statement released Wednesday.

All Nippon Airways, which is currently the largest operator of 787s, with 17 in service, decided to ground all of its Dreamliners after one was forced to make an emergency landing Wednesday morning in western Japan when the cockpit warned of battery problems and a burning smell was detected in the cockpit. Airline executives expressed deep remorse for worrying passengers and family members at a press conference in Tokyo soon after the incident.

This incident came just over a week after a battery pack in a Japan Airlines 787 caught fire after the airplane sprung a fuel leak on the tarmac on Boston's Logan Airport last Monday. The airplane was empty, but it took firefighters 40 minutes to extinguish the blaze. Japan Airlines, which operates 7 787s, had another airplane report a cracked windshield and computer problems earlier this month.

There are currently 50 787s in active service, and Boeing has a pipeline of 800 more orders, with plans to eventually sell 5,000 over the next 20 years, according to the New York Times. The iconic American aerospace firm is betting much of its future on the lightweight carbon-fiber composite jet, which can potentially provide major cost savings to its operators, in the form of reduced fuel costs.

However, these two high-profile failures of its lithium ion battery system, another weight-reducing innovation relatively untested at airplane scale, threaten the long-term viability of the project. As the New York Times reports, an aviation consultant said replacing the lithium ion batteries with more conventional, proven technologies is possible, but would be costly and could double the weight of the airplane's battery system, costing operators more money as well.

Wednesday night was not the first time concerns were raised about using lithium ion batteries in airplanes, according to the New York Times:

"Lithium-ion batteries provide power more quickly than conventional batteries and can be recharged quickly. They are increasingly used in cellphones, computers and electric cars but also have known risks of fires and explosions, particularly if they overheat or overcharge.

While the federal agency has recognized these hazards, it still decided in 2007 to allow Boeing to use them in the 787 as long as the company took a series of protective measures. At the time, the agency noted that 'lithium ion batteries are significantly more susceptible to internal failures that can lead to self-sustaining increases in temperature and pressure' than conventional batteries.

As part of Wednesday’s emergency directive, the government said it would 'validate that the 787 batteries and the battery system on the aircraft are in compliance with the special condition the agency issued as part of the aircraft’s certification.'"

Boeing's chief engineer for the 787 project held a conference call after the Boston incident saying the company was aware of the potential pitfalls and had built in numerous redundancies that would prevent any battery problems from creating a catastrophic threat to an airplane already in flight. Wednesday morning's incident in Japan demonstrated that these safety features were not yet adequate, and raised the most serious concerns yet about the short-term reliability of the new technologies incoroprated in the 787. Other new aircraft like the Airbus A380 have tended to endure growing pains as they are introduced to the market and kinks are worked out, but none have been so severe to require grounding by regulatory agencies.

Boeing's stock price declined 3 percent Wednesday, and a further 2 percent in after-hours trading.

Reach Executive Producer Matt Pressberg here.