He said nine bodies had been identified by their uniforms.
Local military commander Binsar Sianipar, who led the mission, said bad weather hindered the retrieval of the bodies using ropes and it will resume early Saturday.
The helicopter lost contact five minutes after takeoff from Oksibil, the capital of the district of Bintang Mountain on June 28. It was traveling to the provincial capital, Jayapura.
The army helicopter was taking troops and supplies to a border post in Okbibab near Papua New Guinea and had refueled at Oksibil before it was reported missing by the control tower, the military said.
The search had resumed after residents of the village of Oksop told authorities last week that they had seen the wreckage in an area considered sacred, about 12 kilometers (7 miles) from Oksibil.
Flying is the only practical way of accessing many areas in the mountain and jungle-clad easternmost provinces of Papua and West Papua where military helicopters recently have become a target of separatist rebels.
Papua, a former Dutch colony in the western part of New Guinea, was incorporated into Indonesia in 1969 after a U.N.-sponsored ballot that was widely seen as a sham. A small, poorly armed separatist group has been battling for independence since then.
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