CHRIS UHLMANN, PRESENTER: Protected dugongs and sea turtles are being cruelly slaughtered in Queensland's Torres Strait to supply an illegal meat trade.

An investigation by 7.30 has found deeply confronting footage that we are about to air. It shows the brutal methods used to hunt the animals, with turtles being butchered alive and dugongs drowned as they're dragged behind boats.

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

And a warning: this report by Sarah Dingle and producer Lesley Robinson contains disturbing images and coarse language.

SARAH DINGLE, REPORTER: At the northern-most tip of Australia lie the serene islands and waters of Queensland's Torres Strait, the birthplace of Native Title. But on those beaches, there's a slaughter underway.

7.30 travelled to far North Queensland where IT entrepreneur turned eco warrior Rupert Imhoff has been investigating the fate of threatened turtle and dugong populations. And what he found is shocking. A turtle lies tethered for up to three days, waiting to die.

RUPERT IMHOFF, ECO WARRIOR: They dragged it out of the water, flipped it on its back. You could see it was already terrorised. It was flapping around madly. And they came up with this concrete block and basically tried to slam it in the head, obviously to stun the animal. Didn't quite work.

SARAH DINGLE: The images become even more confronting.

RUPERT IMHOFF: Before they started hacking off its fins, they wanted to check if it was pregnant, and sure enough this turtle was a mature aged turtle. Had up to 125 eggs in it. It was gonna be the next generation of turtles, but they decided to cut it up right there and then.

SARAH DINGLE: Even as it's hacked, the turtle clings to life, apparently in agony for seven and a half minutes.

RUPERT IMHOFF: Didn't actually die until they took off the bottom shell, they actually peeled off the shell and then it just let out one gasp - one last gasp of air and passed away.

SARAH DINGLE: Using a hidden camera, Rupert Imhoff spent two weeks in the Torres Strait filming the hunting of sea turtle and dugong which are both listed as vulnerable to extinction.

RUPERT IMHOFF: They go out, they spear them at sea, they then tie the tail to the back of the boat and they hold the head underwater. And it can take up to seven and a half minutes again, so I've been told, for that dugong to drown.

SARAH DINGLE: Here, a dugong is methodically carved up for consumption. For anyone else, this kill would be illegal, as dugong are protected under federal law. However, the Native Title Act allows traditional owners to hunt to satisfy their personal, domestic or non-commercial communal needs.

Anywhere in Australia, this horrific cruelty would be will illegal. But in Queensland alone, Native Title hunting is exempt from animal cruelty laws. Animal rights activists are appalled.

Lawyer Rebecca Smith was a paid consultant on the turtle and dugong hunt for the Torres Strait Regional Authority.

REBECCA SMITH, LAWYER: Most conservation groups won't touch this issue. It's just too hard, too prickly, too sensitive. It's often deemed - people who are opposed to traditional hunting are often called racist, but there's nothing racist about saying, "This is cruel. We'll move on from there. We'll do this humanely now. We've progressed."

SARAH DINGLE: Aerial surveys of dugong and turtle numbers are imperfect and no-one knows exactly how many there are. Green sea turtles face an extra pressure. They're by far the turtle species most intensively hunted for their meat. But locals say there are bigger threats for turtle and dugong.

???: You know we are under threat from pig predation, our - one of the greatest, biggest rookeries in the Southern Hemisphere on Cape York, Rain Island, is under threat from climate change, but we seem to be concentrating I think far too much on, you know, Indigenous people hunting them.

SARAH DINGLE: What is known is that the Great Barrier Reef is a last stronghold. It's home to the biggest sea turtle rookery in the globe and one of the world's largest population of dugong.

Cairns-based Colin Riddell calls himself "The Dugong Man". A former abattoir worker, he's an unlikely but tireless campaigner for animal rights.

COLIN RIDDELL, ANIMAL RIGHTS CAMPAIGNER: I have to pursue it to the end because otherwise the end may be for the animals.

SARAH DINGLE: Colin Riddell's investigations have revealed the slaughter goes on far to the south in coastal Queensland waters.

Green Island is one of the jewels in the crown of Cairns tourism. We've been told just last week at this spot Indigenous hunters chased down and took a green sea turtle in full view of shocked tourists. There's no way of knowing where those hunters came from, but locals say this is a weekly occurrence on this island.

STEVE DAVIES, TOUR OPERATOR: They can be out there a lot, you know - three, four, five times a week. They come across in quite large tinnies with large outboard motors on board and they chase the turtles till they're completely and utterly exhausted.

SARAH DINGLE: The culture clash between hunters and tourists has led to heated confrontations.

INDIGENOUS HUNTER (Amateur video): This our land! We don't list end to your shit, mate! We can do anything on this land we wanna do, mate!

SARAH DINGLE: This video was shot two weeks ago by a tourist and given to 7.30. It shows an allocation between a tour boat and three Indigenous hunters.

INDIGENOUS HUNTER (Amateur video): Ya just don't tell us what to do on our land! You're not from this f***in' land; we are! We're the traditional owner! We own every f***in' reef around here, mate!

SARAH DINGLE: It's not clear what they're hunting for, but there's no mistaking the tensions.

INDIGENOUS HUNTER (Amateur video): You f*** off back to your country. This is my country, c***.

SARAH DINGLE: Is there a sense in your area that the Indigenous hunters are untouchable?

STEVE DAVIES: Without a doubt. And they believe they're untouchable.

SARAH DINGLE: But there are conservation efforts.

Well away from the glitzy marinas and the tourist strip, here in the industrial area of Cairns is the town's only turtle rehabilitation centre. It's run on the smell of an oily rag. Here, injured and starving turtles are treated and brought back to full health.

Today, Jenny Gilbert and her team are readying a 180 kilogram breeding age female green sea turtle for release. By the look of things, this 80-year-old turtle has already survived a number of hazards.

Turtles like this are being hunted not traditionally, but for a very modern purpose. Our investigations have revealed the hunt is feeding a flourishing black market.

JAMES EPONG, MANDUBARRA LAND & SEA CORP.: Well nine times out 10 the illegal trade is to sell the meat for the benefit - for grog money or drugs.

SARAH DINGLE: And can you can make a buck out of it?

JAMES EPONG: Yes. There's one person that we know of in Yarrabah made $80,000 one year.

SARAH DINGLE: James Epong is a Mandubarra man who lives on his traditional lands an hour south of Cairns and Yarrabah. The Mandubarra have declared a moratorium on taking turtle and dugong from their see country, but around them, the illegal meat trade continues.

JAMES EPONG: I myself went to a pub on a Friday afternoon to go and have a coldie with one of me mates and was approached by some other Indigenous people with trivac (phonetic spelling) meat for sale, which was turtle and dugong.

SARAH DINGLE: On four separate occasions 7.30 has confirmed multiple eskies arriving on the afternoon flight from Horn Island to Cairns.

RUPERT IMHOFF: I do not know 100 per cent for a fact what was in those eskies, but I have heard numerous reports and been told by the islanders themselves that they are transporting an excessive amount of turtle and dugong down to Cairns. Now on my flight I think there was about six or seven eskies that come off and I've been told that it almost a daily routine.

SARAH DINGLE: Indigenous sea rangers are employed and equipped by governments to care for marine wildlife. This esky was addressed to a ranger.

RUPERT IMHOFF: From what I understand and what I observed and what I spoke to the islanders about is the head hunters on all these islands are actually the rangers themselves. Now this money has gone into their pockets. It's gonna help them buy outboard motors and help them basically go and hunt these turtle and dugong down in bigger numbers.

SARAH DINGLE: Were any of the people you saw hunting and killing animals rangers?

RUPERT IMHOFF: Yes, they were 100 per cent.

SARAH DINGLE: Did you pay those people in your footage to do what they were doing?

RUPERT IMHOFF: We did not pay a single person any money while we were up there.

SARAH DINGLE: And the illegal trade continues further south.

SEITH FOURMILE, CAIRNS TRADITIONAL OWNER: I know that there's a lot of non-Indigenous people that are doing it as well.

SARAH DINGLE: Are they doing the hunting or are they involved in other way?

SEITH FOURMILE: They're involved with the trading of it, or selling it and passing it down, and some of the turtle meats has gone far down as Sydney and Melbourne.

SARAH DINGLE: And it's not just dugong and turtle meat being sold. Traditional owners from Cape York are pushing to end the indiscriminate slaughter and stop the esky trade.

FRANKIE DEEMAL, TURTLE AND DUGONG TASKFORCE: We don't have that kind of legislative assistance to do that. What do you do when you confront a rogue killer?

SARAH DINGLE: And we've heard a lotta people talk about rogue killers. Who are these rogue killers?

FRANKIE DEEMAL: They're there.

SARAH DINGLE: Who are they?

FRANKIE DEEMAL: They know who they are.

SARAH DINGLE: For those with Native Title rights, customs can change.

LOCAL MAN: We're gonna name this turtle Bumbida (phonetic spelling), after our grandmother.

SARAH DINGLE: But the Mandubarra people at least have sworn to protect these animals.

CHRIS UHLMANN: Sarah Dingle with that report, produced by Lesley Robinson.

And 7.30 contacted the Queensland Department of Environment and Resource Management. In a statement it said it takes, "the claims very seriously and will investigate all reports of illegal hunting and poaching".

You can follow the progress of the turtles released in this story by going to the sea turtle satellite tracking page.

Editor's note: (April 16) the ABC also approached the Torres Strait Regional Authority (TSRA) several times over the course of a week prior to broadcast but their spokesperson was unavailable for comment.