The Indonesian Consul in the northern Australian city of Darwin says he is concerned about the number of Indonesian nationals detained for alleged illegal fishing in Australian waters.

Harbangan Napitupulu says many of the fishermen he has spoken to believed they were in Indonesian territory when they were arrested.

The consul says more than 250 fisherman are in detention in Darwin, including 24 people under the age of 18.

He says at least half of them were "shocked and confused" when they were detained by Australian authorities.

"We have been informed by fisherman that were caught for the last two months that most of the them were caught out of the situations that they are not aware that they are already in Australian territory," he said.

Harbangan Napitupulu says one Indonesian captain is mounting a legal challenge to his arrest and detention, and it is possible others will follow.

He also says the detainees fear for the economic survival of their families, who rely on the money they send home to buy food.

"They were very disappointed with the way they were treated starting when they were caught at the sea and they are thinking of how their family can survive," he said.

The Australian Fisheries Management Authority says there's about a 99 per cent conviction rate for those charged with illegal fishing in the Australian zone.

A spokesman, Nigel Catchlove, says there are only a small number of cases where the fishermen are arrested and detained in Australia and released without conviction.

"We let those people go, we give them back their boats," he said.

"If those boats have been destroyed as being unsafe or a threat to human life we do compensate them for that."

Produced by Radio Australia and Australia Network