The FAA reports the aircraft crashed two miles off the shore of Indian Wells Beach in Amagansett just before 3 p.m. Saturday.
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The plane was a Piper PA31 Navajo twin-engine aircraft with four people on board including the pilot, reports the Coast Guard.
The plane was en route to East Hampton Airport, when it appears to have flown directly into a thunderstorm. When the plane fell off the radar screens, controllers called police.
The NTSB has yet to determine the exact cause of the crash.
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Authorities are refusing to identify the victims who were pulled from the water.
The Coast Guard will continue to search throughout the night for the two missing passengers on board the plane.
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