An illegal toothfish fishing vessel New Zealand authorities were pursuing has been captured and blown-up by the Indonesian Navy.

The stateless Viking was one of a fleet of six illegal and unregulated fishing vessels plundering toothfish stocks in the Southern Ocean and was the last to be apprehended.

Fishing in the area is banned by an international convention to conserve Antarctic marine life.

ADENG BUSTOMI/REUTERS The Viking was a stateless vessel, falsely claiming to be flagged under Nigeria.

New Zealand's pacific fisheries ambassador, Shane Jones, said New Zealand had played a "critical role" in ridding the area of the pirate vessels.

READ MORE: NZ navy intercepts toothfish poachers

Viking was apprehended in Indonesian waters and blown-up by the Indonesian Navy and the Ministry of Maritime Affairs and Fisheries in the waters of Tanjung Batumandi, Pangandaran, West Java, on Monday.

The crew was being detained in Indonesia.

Jones said the dramatic way in which the vessels had been driven out of business would "certainly put a dent in the business of illegal fishers".

But he said they appeared to have been poaching fish for a long time and he couldn't guess whether or not the fleet's shadowy operators might still have come out on top financially.

"The forces that underwrite illegal fishing are like 'rust'. You have to constantly chase it out of your system," he said.

Ministry for Primary Industries compliance operations manager Gary Orr said New Zealand authorities had been working with a range of countries for the past year to capture the six vessels and their crews.

In December, New Zealand authorities patrolling the Southern Ocean captured video and still footage of illegal vessels and provided crew lists to other countries involved in the crackdown.

Jones said the "most frightening prosect" for the fishing industry was now a "largely unregulated" fleet of more than 3000 longline fishing vessels operating just north of the Kermadec Islands.

"On computer screens you can see so many longline vessels that it resembles an 'afro'. It is not fair to say all of the vessels are operating in an illegal fashion but ... the obligation on them is to operate within the fishing rules and policies of the state whose flag they are flying.

"New Zealand tuna fishermen end up with the dregs and they are currently stewing about it," he said.

The Viking was a stateless vessel, falsely claiming to be flagged under Nigeria.

"What we're seeing is fraudulent documentation in relation to the vessel flag," Orr said.

The nationalities of the Viking's crew were not known.

Had it been caught in New Zealand waters, the vessel would not have been blown up, he said.

None of the vessels had been caught in areas under New Zealand jurisdiction, he said.

"Our engagement in these vessels has all been on the high seas where you're operating under international law where it's not so clear cut."

Vast amounts of time and resources had been spent on pursuing the fleet, but Orr could not say how much it had cost New Zealand taxpayers.

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