Ron and Maria Passi, who operate Murray Island's only taxi, were out driving the night the king tide struck. Neighbours flagged them down, asking for help, and so it was not until some time later that they saw their own grandchildren standing in the road. "They were shouting 'Granddad, stop the car, the water is coming in the house'," says Ron. "I just slammed on the brakes."

The couple's son, Sonny, was outside his fibro shack with his five children, watching the monster surf, lashed by north-west winds, rise ever higher. In the commotion, everyone had forgotten that Sedoi, the baby, was still inside. They heard her crying and found her in her cot, covered in sand. Water had surged in after a wave picked up a big wooden pallet and flung it through the front wall.

No one on Murray had ever seen such a high tide before. Other islands in the Torres Strait, which lies between the far north-eastern tip of the Australian mainland and Papua New Guinea, have witnessed similar scenes in recent years. Houses, roads and graveyards have been flooded, and the locals believe they know the reason: climate change.

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The low-lying islands that dot the sparkling waters of this region are facing similar challenges to South Pacific nations such as Kiribati and Tuvalu. But while the plight of those countries is well known and is regularly discussed in the international arena, few people outside Australia have even heard of the Torres Strait. Even Australians would have difficulty locating it on the map, and the remote islands – accessible only by light plane – receive few visitors.

Donna Green is one exception. A scientist at the University of New South Wales, English-born Dr Green is educating the islanders about the possible impacts of climate change and ways in which they can adapt. She embarked on the project after discovering that no one else was doing it. In fact, although the Torres Strait is considered the most vulnerable area of Australia, it is barely on the radar, either as a subject of scientific research or a focus of government policy.

There is no action plan for the region, and the newly formed Department of Climate Change was unable to cite any studies relating to these northerly islands. A search for the words "Torres Strait" on the department's website yields no results.

Until the end of the last Ice Age, the strait was a land bridge connecting northern Australia with New Guinea. Some islands lie only a few miles off the Papua New Guinea coast, and the locals have more in common, ethnically, with the Melanesians of Papua New Guinea than the Aborigines of the Australian mainland. But they consider themselves proud Australians, and feel mildly aggrieved that it is not widely known that Australia has not one, but two indigenous races.

Six of the inhabited Torres islands are low-lying coral cays or swampy mud islands, with little or no elevation. As you fly over them, they look like smudges of green in a shimmering expanse of blue. Others are granite or volcanic, with some higher land. Even there, though, people are accustomed to living by the beach, their days revolving around fishing and collecting shells.

At dusk, walking along the water's edge on Murray Island, the scene is idyllic. A local man is fishing for mackerel with his young son, as shoals of sardines dart along in the shallows. Children play in the sand, and reggae music drifts from one of the simple houses built along the beachfront, in the shade of coconut palms and almond trees.

But, after generations of living by the sea, many locals no longer feel comfortable. Maria Passi says: "At night I can't sleep if the tide is high." Her house was flooded by the king tide as well as her son's. "There was water everywhere, and rubbish floating around, and coconuts under the bed," says her husband Ron, as his wife adds: "When I saw how it looked, I just sat down and cried."

Abnormally high tides are not the only phenomenon that the islanders have observed. The seasons are shifting, and the land is eroding. Birds' migration patterns have altered, and the turtles and dugongs (sea cow) that are traditionally hunted for meat have grown scarce. People are no longer certain when to plant their crops: cassava, yams, sugarcane, bananas, sweet potato.

Murray, home to about 400 people, is the birthplace of indigenous land rights. It was five Murray Islanders, led by Eddie Mabo, who brought a legal action contesting the idea that Australia was uninhabited and belonged to no one when the British arrived. After a landmark High Court decision in 1992, Aborigines and Torres Strait islanders regained ownership of their traditional lands. But now the land for which Mr Mabo fought so long and hard is being swallowed by the sea.

Dr Green has organised workshops on the islands, offering information and practical advice. She has also held meetings with community elders in order to record their observations of weather patterns and environmental changes, in a project that blends traditional knowledge with Western science.

"There are very few formal records for this area, but the people who have lived here for generations have got these amazing banks of knowledge in their heads," Dr Green says. "If we can understand the past, through people's memories of extreme weather events, for instance, we can make projections for the future and work out what kind of action needs to be taken.

"Some of the people I've spoken to have already passed away. So that knowledge of theirs, which is like a library, is already being lost and it's irreplaceable."

Ron Day, a Murray Island elder and community leader, says he has witnessed disturbing changes. "We see the big trees near the beach, like the wongai trees, falling down. The seagrass that the dugongs eat, you used to find long patches of it, but not any more. The corals are dying, and the sand is getting swept away and exposing the rock.

"We were taught by our grandfathers and fathers to read the sky and forecast the weather. You see this cloud, you go to your garden and start planting. You see that cloud, it's time to clear your land. But nowadays the weather is unpredictable."

Others report that the rainy season is rainier, the dry season drier. And the marine life is behaving oddly. Julie Zaro, administration officer at the school on Murray, says: "Normally, at this time of year, you just throw out a line and get a mullet. But I sat there all weekend and didn't see one fish. When it's turtle time [the mating season], you usually see hundreds of them up on the beach, laying their eggs. But this year I saw only five or six."

The people of this area – already socially and economically marginalised – face an uncertain future. Yet they barely figure in the Australian climate change debate, which has largely focused on the prolonged drought and its impact on farmers. About 7,000 people live on the islands, 18 of which are inhabited. Some want an evacuation and relocation plan; others are determined to stay put. They have a visceral connection with their land, and fear that their identity and culture will be extinguished if they are dispersed.

In the absence of any significant outside assistance, individuals are taking the initiative. On Murray, some locals have built makeshift fortifications against the waves, using fallen tree trunks, beach debris, rubber tyres and concrete blocks.

Mr Day is encouraging the islanders to move to higher ground. "We're sea people, and the sea is in our blood," he says. "But living on a small island surrounded by ocean, it's very dangerous. We have to face facts: the water is rising."

One of his fellow islanders, Sarie Tabo, is considering relocating. "But it would be very hard for me, because I fish every morning and every afternoon," he says. "I wake up and I go to sleep with the sound of the waves. Up on the hill, it would be a whole different way of life."

At least he has that option. On islands such as Saibai, there is no high land to move to. The islanders are squeezed on to a narrow strip of ground, between the encroaching ocean and the encroaching swamp. They have raised their houses, and sandbagged their families' burial plots. The sea wall gets washed away during floods.

Father Ezra Waigana, priest of St Matthias Church on Saibai, says: "We were told there's an iceberg melting and the level of the sea is going up. We don't know how we will survive. Our island is only flat, and the water seems to be taking all the land."

There was an exodus from Saibai after a major flood in 1948 but elders of Mr Waigana's clan decided to stay on, in the place where their ancestors are buried. Their descendants feel it would be disrespectful to move – and some people cite God's promise to Noah never again to flood the Earth.

Politicians from Canberra and Queensland occasionally fly into the islands and fly out. The locals call them seagulls. Asked whether the government is doing enough to help, Mr Day replies: "Most of the time they play deaf." The islanders, he says, "need to make ourselves known to people in the global village".

Dr Green says: "It's been said to me by some islanders that they're very happy that the Australian government is investing in the Pacific, to help their brothers and sisters deal with the impact of climate change. But they wonder why the government is not more strongly investing in similar communities in Australia, and they feel a bit overlooked.

"This is an area with few resources, and limited capacity to adapt, and it does seem a little forgotten at the moment. But these problems are not in Australia's backyard. They are right in the front room."