Twenty Indonesian men who were apprehended while fishing illegally in waters off Western Australia's north have been sentenced in a Northern Territory court.

The ABC reported earlier this month that a traditional owner and tour operator had led Australian Border Force (ABF) officials to four foreign fishing vessels in the mangroves of Kuri Bay, about 220km north of Derby.

The ABF later confirmed three of the four boats had been destroyed at sea, with 20 of the 33 fishermen taken to the Australian mainland for prosecution.

A haul of 700kg of sea cucumber, 4kg of shark fin, 4kg of sea urchin and 2,450kg of salt was found on the boats.

The incident led to a national debate over Australian's maritime policies, with the biosecurity threat highlighted by farmers.

Eleven Indonesian men faced Darwin Local Court on Thursday, with all pleading guilty to using a foreign boat to fish in territorial sea.

One fisher, believed to be a captain, was sentenced to one-month jail, which was suspended for two years.

A second man was fined $300, while the other nine were fined $150.

All 11 received recognisance orders, meaning a fine of $1,000 or $2,000 would apply if found guilty of similar offences in the next one to two years.

On Friday, the remaining nine Indonesian men also faced Darwin Local Court.

Two men were fined $4,150, another $300 and the remaining six all fined $150.

Recognisance orders were also placed against these nine men, with fines of up to $2,000 payable if the men reoffend in the next one to two years.

Peter Tucker, who assisted authorities with locating the four vessels earlier this month, is concerned the penalties do not go far enough.

"The fact that in my business, if I do something that is not within my licences, I can be fined and even have my business taken away from me," he said.

"And here we have these people coming in for months at a time no doubt, and they get a slap on the wrist.

"I think the government needs to enter much more serious negotiations with Indonesia itself and be much stronger about protection of our borders, our waterways, our marine environment."

An ABF spokesperson would not comment on the case due to privacy obligations, but said illegal fishing crews were removed from Australia "at the earliest opportunity" once prosecuted.

"We are committed to protecting our vulnerable marine resources and delicate ecosystems through the targeting of irregular foreign fishing in Australian waters," the spokesperson said.