Protected dugongs and sea turtles are being cruelly slaughtered in Queensland's Torres Strait to supply an illegal meat trade, an investigation by ABC's 7.30 has found.

The program has aired confronting footage that shows the brutal methods used to hunt the animals, with turtles being butchered alive and dugongs drowned as they are dragged behind boats.

The investigation throws into sharp relief the conflict between Indigenous Australians and animal rights activists over traditional hunting methods and exposes a black market in animal meat.

Activist Rupert Imhoff spent a fortnight in the Torres Strait, filming the hunting of the turtles and dugongs, both listed as vulnerable to extinction.

He used a secret camera to film scenes of animal cruelty, including the slow death of a sea turtle.

"It didn't actually die until they took off the bottom shell, actually peeled off the shell," he said.

"And then it just let out one last gasp of air and passed away."

Both dugongs and turtles are protected by federal law, but the Native Title Act gives an exemption to traditional owners, who can hunt to satisfy their personal, domestic or non-commercial communal needs.

The traditional hunting methods are seen by animal activists as deeply cruel but Queensland exempts native title hunting from its animal cruelty laws.

'Too sensitive'

Lawyer and advocate Rebecca Smith says conservation groups avoid criticising Indigenous hunting.

"It's just too hard, too prickly, too sensitive," she said.

"It's often deemed people who are opposed to traditional hunting are often called racist, but there is nothing racist about saying this is cruel."

National Indigenous radio broadcaster Seith Fourmile is a passionate advocate of the Indigenous right to hunt. He has nothing to do with the scenes of animal cruelty exposed by 7.30.

"We're working with the RSPCA to actually look at that cruelty to animals," he said.

"But it has got to be a cooperative approach."

The slaughter in Australia's north goes well beyond the bounds of traditional hunting.

Former abattoir worker Colin Riddell has spent years collecting evidence of dugong and turtle killing. His investigations reveal the killing goes much further south in Queensland's coastal waters.

James Epong is a Mandubarra man who lives on his traditional lands an hour south of Cairns.

The Mandubarra have declared a moratorium on the taking of turtle and dugong, but around them an illegal meat trade flourishes.

"Nine times out of 10, the illegal trade is to sell the meat for the benefit, for grog money or drugs," he said.

"One person that we know of in Yarrabah made $80,000 in one year."

Mr Fourmile says there are also non-Indigenous people involved in the illegal trade.

"They are involved with the trading, with selling it, passing it down - some of the turtle meat has gone as far south as Sydney and Melbourne," he said.

In the Torres Strait, Horn Island appears to be a transport hub for the illegal trade. On four separate occasions, 7.30 has confirmed multiple eskies arriving on the afternoon flight from Horn Island to Cairns.

'There's no jobs'

All the Indigenous people interviewed by 7.30 recognised the illegal trade and are committed to ending it.

"There's no jobs on Aboriginal community, let's not lie about it," Mr Fourmile said.

"There's no doubt this is happening. I'm not going to lie about the fact that there is some people out there doing it."

Cape York saltwater people like Frankie Deemal are working to end the esky trade.

"We don't have no legislative framework in place in which we can police the kind of rogue killing, the kind of outsiders coming into our place," he said.

"We don't have the kind of legislative assistance to do that."

And the Mandubarra people are helping to protect the turtle that has helped sustain them.

"I went out to get one where I normally go and there was just nothing there," said James Epong.

"I came home empty-handed and I thought, 'I can't have this'. I want my kids to experience what I'd experienced. So from that day we just said no more hunting."

For the Mandubarra people, the turtle hunting ended in 1993.

Queensland's Department of Environment and Resource Management was contacted by 7.30.

In a statement, the department said it "takes the claims very seriously and will investigate all reports of illegal hunting and poaching".