Boat driver Suribabu, assistant driver Bairava Swami and helper Rama Rao are also facing charges of negligence, which caused the tragedy.
The whereabouts of the three crew members of the private boat that capsized in Krishna river at the Pavitra Sangamam remained a mystery two days after the accident.
The family members of three crew members confirmed that it did not belong to any of them, the police said.
Speculation is rife that the trio had jumped out of the boat and swam away when the situation went out of control.
Chief Minister N. Chandrababu Naidu said in the Assembly one of the bodies was identified as that of Bairava Swamy.
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