Watchdogs have called for better safeguards for fish stocks in international waters off Australia after the revelation that authorities confiscated a 130km fishing net off Antarctica this year.

The huge gillnet, found at Banzare Bank roughly 4000km south-west of Perth, had 29 tonnes of Antarctic toothfish, wildlife monitoring organisation TRAFFIC reported yesterday.

Gillnets, nicknamed "death curtains", snare big fish by the gills and are banned under the treaty governing Antarctic fishing.

The nets, which stand several metres high and are weighted to the seabed, can become "ghost nets" that continue to kill fish if lost and left in place.

The confiscated net was found in April by crew on the Customs vessel Oceanic Viking at a depth of 1500m before the ship hit headlines for the current asylum seeker stand-off.

Perth-based Antarctic fisherman Martin Exel was called to deal with the net, which was created from nine separate sections.

His trawler Southern Champion was only able to haul in 9km of the net and he destroyed the rest.

Mr Exel said two vessels were in the area at the time but neither owned up to casting the net.

He said it was frustrating that gillnets were being found in the Southern Ocean but praised Australian authorities for their willingness to crack down on illegal nets in international waters.

It also emerged this week that European Union officials granted permits to two Spanish vessels to deploy gillnets in international waters between Australia and New Zealand.

Deepwater gillnets are yet to be banned in much of the southern hemisphere because there is no international body to regulate southern fisheries.

TRAFFIC's marine program manager Glenn Sant said gillnets seriously undermined the conservation of toothfish and other species such as deepwater dogfish and school shark, which were widely used as sources of fish oil.

Mr Sant urged governments to ban fishing vessels from even carrying gillnets, particularly to protect toothfish stocks, which have been seriously depleted by overfishing.

Federal Fisheries Minister Tony Burke said officials would "take up the issue with EU representatives in a bilateral meeting in Auckland next week".

The meeting will move to create a body called the South Pacific Regional Fishing Management Organisation to regulate southern fisheries in international waters.

Australian and New Zealand delegates are expected to express anger at the EU for breaching a casual agreement not to establish any new fisheries before this organisation was created.