For almost a decade, Torres Strait Islanders have been lobbying the Federal Government for funding to build seawalls.

There are six low-lying islands that are inundated a few times a year, during king tides.

Currently, they have no way of protecting their villages from the tide and it is causing serious damage to homes, roads and the sewerage system.

According to climate projections by the CSIRO, the situation will get worse as the region becomes warmer and sea levels rise further.

University of New South Wales scientist Donna Green has researched climate change in the area and says the inundation that is happening only a few times a year now, will become much more frequent.

"Projections would suggest that one of their worst high tides, for example, a one in 100 year event, may occur as much as once in every few days in 40-50 years from now," she said.

"So it's a big difference if it's a community that can deal with inundation that is very bad, but very occasional, that's something you can maybe manage. If it's occurring more frequently, that becomes a real problem for daily life."

Dr Green says of her many visits to the low lying islands, it was on a trip to Saibai in 2010 that she experienced the worst flooding.

"We were walking around in knee to thigh high water. Not just in water right at the edge of the shoreline, we were walking around through the school, through the shops," she said.

"It was quite odd, because you can have a lovely sunny day, and everything else looks good, but there's just something very wrong when you've got an awful lot of water slowly encroaching over the seawall, and filling up areas that clearly should be dry."

The elders on Saibai say they have already lost up to 200 metres of beachfront because of erosion.

Numerous engineering reports on how to resolve this situation on Saibai have concluded that urgent action is needed.

Angus Gordon, a coastal engineer with 40 years experience, recommended in 2008 that seawalls were needed.

The Torres Strait Council followed Angus Gordon's recommendation with its own four year strategy paper, costing the required works on the six islands at $22 million.

According to the council, this solution is not permanent but will give the communities an extra 20-30 years.

However this paper was shelved in Canberra and ignored.

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Flooding from king tides has become a regular occurrence.

One of the worst was three years ago when the sewerage system on Saibai was inundated and raw sewage spilled into the sea and into fresh water lagoons.

The environmental health officer on Saibai, Keri Akiba, wrote a report at the time, documenting an unbearable smell. He says it suffocated the community and created a serious health scare.

Keri Akiba says, as a result of more frequent flooding events, the mosquito population has multiplied.

Saibai island is already mosquito-prone because of its swampy landscape. It is home to the Anopheles Farauti vector which can carry the malaria parasite.

Queensland Health figures obtained by Background Briefing show that malaria cases in Saibai are on the increase. Last year, the community has had its worst malaria outbreak in 50 years.

Entomologist with Queensland Health, Dr Greg Devine, says there is a connection between the inundation from the tide and the growing mosquito population.

"Once that seawater and freshwater from rain mix together they produce a kind of a brackish environment which is particularly good for Farauti [mosquito]," he said.

"So in a place like Saibai, which so much of its territory is under water for so much of the time, there's a huge breeding pool for this mosquito."

Dr Devine has now travelled to Saibai with a team of entomologists to investigate.

Meanwhile, people in Saibai have started wondering whether plans are quietly being made for them to be relocated.

Torres Strait Mayor Fred Gela says that is unacceptable and would be resisted.

"We'll be waiting to see which government is going to come into the Torres Strait to look at relocating my people. Because they'd want to bring an army," he said.

A spokesman for Minister for Regional Affairs Simon Crean said in a statement he is unaware of any relocation plans.