Fifty-five Indonesian fishermen have been cleared of illegal fishing off Australia's northern coast.

Federal Agriculture Minister Tony Burke told parliament the group will be transferred from a detention centre in the northern city of Darwin to a motel, and will be sent home on Saturday.

Mr Burke says five of the men's boats were destroyed when they were apprehended last month, and says the fishermen will be compensated.

"As can be the case in any law enforcement activity, genuine errors can be made," he said.

"The Indonesian consulate is expected to provide travel documents for this group by noon tomorrow to assist their return to Indonesia."

The Indonesia Consul in Darwin is happy with the outcome.

Harbangan Napitupulu says investigations into other Indonesian boats apprehended in April are continuing.

He says he was surprised 33 boats were seized in just three weeks.

"We felt that perhaps there was something wrong with these apprehensions," he said.

He said many of the detained fishermen believed they were in Indonesian waters when they were detained.

Produced by Radio Australia and Australia Network