The number of resident dolphins in Darwin Harbour has almost halved since construction of the huge Inpex liquid natural gas plant and shipping channel began in 2011.

Key points: Humpback dolphin numbers have dropped by almost 50 per cent

Humpback dolphin numbers have dropped by almost 50 per cent Scientists have no funding to find out why populations are declining

Scientists have no funding to find out why populations are declining Inpex says its gas plant construction is not to blame

But Northern Territory government scientists who have recorded the drop have not been able to find out why numbers have fallen, and suspect several causes.

The harbour is home to three small, tropical coast-hugging species, some of which are endemic to Northern Australia.

The Australian snubfin is officially classified as near threatened, while the Australian humpback dolphin and coastal bottlenose dolphin are vulnerable to loud noise and fluctuations in the availability of fish.

NT Environment Department senior scientist Carol Palmer has seen a gradual decline in the harbour's dolphin numbers since she started monitoring them in 2011.

"For the Australian humpback dolphin, where we've got the best data, they've been the most seen within Darwin Harbour, and the populations have dropped from about the mid 40s, down to in the 20s," Dr Palmer said.

NT Government researcher Carol Palmer is frustrated she is seeing dolphin numbers decline without the means to research why. ( ABC News: Jane Bardon )

Declines across all species

Her research shows the humpback dolphin population in Darwin Harbour have dropped from 42 in 2011 to 26 in 2016 and down to 24 last year.

Her data for the wider Darwin region, Shoal Bay and Bynoe Harbour, shows humpback dolphin numbers have dropped across the area from 88 in 2011 to 50 in 2017.

The bottlenose dolphin population in the Darwin region dropped from 28 in 2011 to 23 in 2016. And in 2017 the scientists could not find enough bottlenose to make a count.

Darwin region snubfin dolphin numbers have dropped by almost a third from 32 in 2011 to 24 last year.

The researchers found the numbers of calves in pods of humpback and bottlenose dolphins had declined overall since 2011, but there wasn't a drop in the number of snubfin calves.

"With these coastal dolphins, where you're born is where you live," Dr Palmer said.

"The populations are naturally really small. They're long lived, they're slow breeding.

"So once you get a decline of just one to three breeding females, that can be enough to decline these local populations. It's a very difficult thing to manage."

Carol Palmer has painstakingly identified and catalogued the Darwin Harbour's dolphins. ( ABC News: Jane Bardon )

Dr Palmer has only been funded to monitor the dolphin population declines. She has no funding to research what has caused them.

"It just gets really tricky when there's not a combination of monitoring and research," she said.

"We actually need to be doing applied research and monitoring, not just a statement, but actually be doing it."

Without that research, the Government's scientists have only been able to guess at what is causing the dolphins to disappear.

"Potentially increasing underwater sound, prey availability, and a number of issues to do with climate change [are causing it]," Dr Palmer said.

"In 2016 we had the highest-recorded sea surface temperatures in Darwin Harbour, and across Northern Australia, and we know from work done overseas that can affect fish breeding and prey availability.

"And we don't really understand the influence of shipping and a whole range of things."

Darwin Harbour has become progressively more busy with shipping since 2011. ( ABC News: Jane Bardon )

Inpex funded monitoring

The Territory Government's dolphin numbers monitoring program has been funded by Inpex since 2011, under an agreement made during the environmental approvals process for the Ichthys LNG gas plant in 2011.

It was part of a promised $91 million environmental offset program.

The company told the ABC it had so far provided $2.7 million for dolphin and other marine animal surveys, and $600,000 more would be spent before the end of the dolphin project in 2020.

"The dolphin monitoring program results … found no impact to dolphins attributable to the project's activities," Inpex said in a statement.

"Inpex is committed to … complying with all requirements to minimise environmental impacts including dolphins and coastal marine animals."

Dr Palmer said there was no evidence the gas plant has had an impact on dolphin numbers in Darwin Harbour.

And she said the population declines had also happened at the two other monitoring sites.

"So there seems to be a wider picture of something going on. Darwin Harbour is a commercial shipping area, Bynoe not so much, and Shoal Bay isn't," she said.

"And this is where climate change and sea surface temperature rises could be having a much wider impact than we know."

In their latest Coastal Dolphin Monitoring Progress Report, Dr Palmer and her research colleagues noted that factors which have an impact on dolphin populations include habitat loss, underwater noise, commercial and recreational fisheries, boat strike and climate change.

Tour operator Jim Smith wants more protection of Darwin Harbour. ( ABC News: Jane Bardon )

'Maybe it's a death of a thousand cuts'

Jim Smith, one of the harbour cruise business owners who is dependent on the local wildlife, called on the Territory and Federal governments to fund research into why the dolphin populations were declining.

"Ten years ago roughly every three times we'd go out we'd see dolphins. Now we'd be lucky to see them once a month," he said.

"The harbour is more built [up] than it was with industry. Maybe it's a death of thousand cuts — it's not just industry, it's increased boating, it's increased run-off — but to understand that properly, we need more research."

Northern Territory Environment Minister Eva Lawler said the Government had no plan to fund such research, or ask Inpex or the Commonwealth to help do that.

"At this stage it is about the funding that's there and provided through Inpex, and it's literally millions of dollars," she said.

"We want to see the environment on Darwin Harbour be maintained."

The number of Australian humpback dolphins in the Darwin region fell from 88 in 2011 to 50 in 2017. ( Supplied: Carol Palmer )

'Collaboration needed'

Mr Smith said the Government needed to do much more, including protecting part of the harbour as a marine park.

"I'd like to see specifically for the harbour ultimately a plan, not just a policy, where a site like West Arm for example is set aside for animals, not just us," he said.

Dr Palmer said she remained hopeful the dolphin monitoring program would be extended to become broader research, with the Territory and Federal governments, private business and Indigenous ranger groups cooperating to make it happen.

"Marine research is really tough. It's expensive, it's time consuming," she said.

"This is where a collaboration between corporations, the Commonwealth, government organisations and NGOs, which have all the various skills and expertise that we need, is so important.

"Because it is actually the communication and being able to discuss things that makes for good management.

"We don't have to make the same mistakes that have been made on the east coast, in particular."