A conservation group has taken the unusual step of buying a commercial shark fishing licence on the Great Barrier Reef, and will retire it, saving the sharks that it would otherwise be used to catch.

WWF said it was now seeking funds to cover the cost of the $100,000 licence, which gives the owner the right to drag a 1.2km net anywhere along the length of the Great Barrier Reef, targeting sharks. It can also be used for fishing with lines to target other species.

A fisherman holds a juvenile hammerhead shark caught in a gill net. Photograph: Jeff Rotman / NaturePL

WWF said the licence was used to target sharks for 10 years until 2004, when it caught about 10,000 sharks each year.

The move comes as Queensland government figures show shark catches on the Great Barrier Reef almost doubled between 2014 and 2015: from 222 tonnes to 402 tonnes – about 100,000 sharks that year.

WWF-Australia’s conservation director, Gilly Llewellyn, said protecting apex predators such as sharks was particularly important after the unprecedented bleaching event that devastated the Great Barrier Reef this year. A 2013 study showed that removing sharks from coral reefs disrupted the ecosystem, making it harder for reefs to recover.

“After bleaching, algae spreads,” Llewellyn said. “Researchers found that where sharks were removed by overfishing, smaller predators like snapper became more abundant. These snapper kill the algae-eating fish and the algae then overwhelms young coral.”

Australia has been reluctant to protect endangered sharks from fishing. In November 2014 the Australian government agreed to grant 31 species of sharks protection under a UN-administered convention. But two months later, the government opted out of the agreement with respect to five of the species, including two species of hammerhead sharks.

“These enormous nets kill tens of thousands of juvenile sharks each year, including hammerheads which are listed internationally as endangered,” Llewellyn said. “Hammerhead numbers have crashed in Queensland, possibly by 80%.”

Besides catching the target species, these long nets catch almost anything they pass over, Llewellyn said. That includes dugongs, dolphins and turtles.

How often that happens is not known, since while fishers are required to report the by-catch, there is evidence they could be attempting to hide the catches.

This month a dead dugong was found near Townsville, with signs it had been caught in a net.

And in 2010 and 2011, a dugong and a pair of dolphins were found, in a similar area, which looked as though they had been tied up by the tail and weighed down, with fishers attempting to hide the carcasses.