The spokesman said by phone that port authorities lost contact with the vessel after its engine broke down in stormy seas.
News website Detik.com said 108 people were on board the ship which left from Kolaka, on the southeastern side of the island, and was heading across the Gulf of Boni for South Sulawesi. Another report, on Kompas.com, said 122 people were on board.
There was no mention of casualties.