Indonesian authorities are having trouble finding or contacting an asylum seeker boat that is reportedly in difficulty in waters north-west of Bali.

Yesterday, local authorities called off the search for the boat, carrying about 60 people, that was reportedly taking on water near the island of Madura, in Indonesia's search and rescue zone.

The ABC has been in contact with those on board, but Indonesian authorities say they cannot get through to the passengers and say they are confused by the coordinates.

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An Iranian man on board told the ABC the engine was broken and the boat was filling with water.

"Water is coming [in] to the boat... why can't you come now, it's so dangerous," he said.

Local rescue authorities called off the search overnight but resumed it early this morning, hoping the satellite reading would lead them to the stricken boat.

Immigration Minister Chris Bowen says Indonesian rescue authorities are coordinating the search.

"I know the Australian authorities are passing on all information that we have to the Indonesian authorities. The Indonesian authorities have requested no further assistance," he said.