Penang Health Director Azmi Shapie said Melawati would be given counseling before being handed to the Indonesian consulate in Penang.
Crew members aboard the trawler told Malaysia's national news agency, Bernama, that Melawati had waved frantically to draw their attention and was found clad in only her underpants because her clothes had been ripped to shreds.
She cried throughout her three days aboard the trawler, they added.