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The two aircraft - one with 11 passengers and crew, the other with five people aboard - went down over water about 25 to 30 miles (40-48 km) northeast of Ketchikan, according to Coast Guard Petty Officer Jon-Paul Rios, speaking from Juneau.
The crash site, which the FAA said was at Coon Cove near George Inlet, lies in the vicinity of a popular tourist lodge that runs excursions to the nearby Misty Fjords National Monument, about 300 miles (480 km) south of Juneau, Alaska's capital.
One of the aircraft involved was a de Havilland DHC-2 Beaver with five people aboard, and the other was a de Havilland Otter DHC-3 carrying 11 people, FAA spokesman Allen Kenitzer said in an email message, citing information from local authorities.
Rios initially reported 10 people from the two planes were receiving medical care, with six others listed as unaccounted for. He later said three of the missing had been confirmed as dead. The conditions of the six injured victims were not immediately known, he said.
Neither of the single-engine planes was under air traffic control when they collided, and circumstances of the crash were not immediately known, Kenitzer said.