About 200 rescuers were searching today for the four others.
The survivor told rescuers that all five had stayed together, floating on water hyacinth about 2 miles from Samosir island, until yesterday when the current separated them, said Heronimus Guru, the deputy operation director at the National Search and Rescue Agency.
The Eurocopter EC-130 was on a chartered flight from the island in Toba Lake to North Sumatra province's capital, Medan, when it was reported missing about 17 minutes after takeoff.
Guru said Fransiskus Subihardayan, 22, was found today afternoon about 2 miles from the Onan Runggu port.
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"He was found naked and very weak, floating on water hyacinth on the lake," said Guru, adding that the survivor was rushed to a clinic and now is in a stable condition.
It was the second recent air accident in Indonesia.
Earlier this month a DHC-6 Twin Otter plane crashed in eastern Indonesia, killing all 10 people on board.
Indonesia, a sprawling archipelago nation of about 250 million people, has been plagued by transportation accidents in recent years, including plane and train crashes and ferry sinkings.