It was a classic piece of public relations. A week before the budget, the federal government announced it was committing half-a-billion dollars to the ailing Great Barrier Reef, with the immediate aims of enhancing water quality, culling outbreaks of invasive crown of thorns starfish and boosting scientific research funds that might aid the reef’s “resilience”.

There was no mention of climate change. That should not be surprising. The Turnbull government remains at war with itself over climate and energy policy, with many of its own members openly derisive of climate science and questioning Australia’s commitment to the Paris agreement to keep rises in global average temperatures to below 2 degrees Celsius.

That cohort predictably includes former prime minister Tony Abbott and his backers.

“What we have to realise is, there’s no way we’re going to solve this problem by not involving industry.”

Publicly, the government is still supportive of Adani’s Carmichael coalmine, and the government remains roiled over the future of AGL’s Liddell power station, with pro-coal MPs urging Malcolm Turnbull to change competition laws to force the company to sell the station.

Turnbull and his environment minister, Josh Frydenberg, are walking a tightrope: trying not to poke the bear on the party’s right flank by reassuring regional Queensland of its continuing support of coal, while confronting the dire state of the reef and the many more jobs, and seats, which may be in peril on the basis of current trends.

In the past few days, we’ve found out where the government’s money to aid the reef is being directed. It’s not going to the Great Barrier Reef Marine Park Authority, the statutory body that’s entrusted with the reef’s custodianship and advises the government on the care and protection of the marine park.

Nor is it going to the Australian Institute of Marine Science, or the Australian Research Council’s Centre of Excellence for Coral Reef Studies.

Instead, it’s going to the Great Barrier Reef Foundation, a body with six full-time staff and five part-time staff, which generated a turnover of less than $8 million last year. The body is focused on business cooperation.

By its own description, the foundation “started with a small group of businessmen chatting at the airport while waiting for their flight, wanting to do something to help the Great Barrier Reef”. When asked, the government was not immediately able to say who these businessmen were.

The move to direct more than $443 million to this small foundation was so left-field it caught even its beneficiaries off guard. “It’s like we’ve won lotto,” chief executive Anna Marsden told Fairfax’s Peter Hannam. “We’re getting calls from a lot of friends.”

Marsden said the organisation was seeking advice on how to cope with the sudden influx of funds.

In the past few days of Senate estimates hearings, more serious questions have been raised. There was no competitive tender process, and thus no opportunity for the government’s own scientific agencies to apply for the funds. As Labor senator Kristina Keneally summed up: “I am trying to understand how … the greatest single contribution from the government to the Great Barrier Reef in Australian history went to one foundation without a tender process, without advertising, without a competitive process and, it would seem, without an invitation from the government to the foundation to apply.”

To that end, Labor has lodged a freedom of information request. Others have pointed to the foundation’s links to corporate Australia, including fossil fuel behemoths BHP, Shell and Peabody Energy, as well as key banking figures.

“God help the Barrier Reef,” was the blunt response of Professor Terry Hughes, the director of the Australian Research Council’s Centre of Excellence for Coral Reef Studies, who has been indefatigable in his scorn for untested scientific solutions such as sun-shields, underwater fans and anything that fails to address the core issues of global warming and immediate decarbonising of the economy.

Similarly, acting chief executive of the Climate Council Dr Martin Rice described the focus on water quality and culling starfish as “a golden Band-Aid solution, because it’s not really getting to the root cause of the problem with the bleaching, and that’s climate change.

“When you look at emissions, we’ve had three years of emissions rising in Australia, and any true test of effective climate policy comes down to whether our emissions are going up or down. So there is no credible energy or climate policy in Australia … [Our] emission reduction targets of 28 per cent are woefully inadequate; they’re not aligned with the science,” he said.

“If the world was to go with Australia’s Paris commitments, we would be on target for a 3 to 4 degree [increase in temperature], and that’s devastating. We’re not going to see our iconic Great Barrier Reef survive that. And that’s not just an environmental issue; it’s an economic one.”

But not everyone is in agreement about the foundation’s ability to deliver. Its website lists the Commonwealth Scientific and Industrial Research Organisation, the Smithsonian Institution and many of Australia’s sandstone universities as research collaborators, and its International Scientific Advisory Committee also includes Dr Russell Reichelt, chairman of the Great Barrier Reef Marine Park Authority.

Also on the committee is Professor Ove Hoegh-Guldberg, a professor of marine science and director of the Global Change Institute at the University of Queensland. As far back as 1999, Hoegh-Guldberg predicted that the Barrier Reef would lose most of its coral cover by 2040, a claim that caused considerable controversy at the time.

“The shock to me of having predicted in 1999 that the reef was in trouble was to actually live it over the last three years, and it’s not only the reef that we should be worried about,” he says. “It’s the impact that we’re now seeing across ecosystems which we depend on. There’s real questions about food security.”

Ten days before the government’s announcement, the scale of the threat to the Great Barrier Reef – and the calamity it has already experienced – was brutally spelled out in a new paper published by Nature, which The Atlantic described as “a kind of autopsy report for the debacle”.

Terry Hughes was the lead author of a team of 16 international researchers.

Hughes has stated in preliminary findings that one in every two corals had died. Usually, this happens slowly. When subjected to heat stress, coral species expel the algae that both provides them with their colour and with nourishment. If the algae don’t return quickly to recolonise the corals, they starve.

In the waters around and north of Port Douglas, previously the most pristine section of the park, the water was so hot that the corals died more or less instantly. “They cooked,” Hughes said.

“You could say it has collapsed. You could say it has degraded. I wouldn’t say that’s wrong,” Hughes told The Atlantic. “A more neutral way of putting it is that it has transformed into a completely new system that looks differently, and behaves differently, and functions differently, than how it was three years ago.”

Hoegh-Guldberg doesn’t disagree with any of that, but he says that such a dire situation calls for outside-the-square thinking. “The downturn in the reef’s health has been rather dramatic, so we’ve got to start to do things differently,” he says. “I think it’s a welcome addition to what we need to do to solve this problem.”

Hoegh-Guldberg has an edge of desperation in his voice when he speaks to me. I put this directly to him. “That’s a very fair reading,” he agrees.

Hoegh-Guldberg is one of Australia’s most respected marine biologists. He is quick to point out that he sits on the Great Barrier Reef Foundation’s advisory committee. But while political questions remain over the funding, and why it was directed to this small body, he argues the urgency of the situation means the reef’s defenders must work with what they have.

“I think it’s wake-up time. This is not some sort of green-washing exercise by industry. I would not be associated with this if it was. People who are not involved may be sniping, and scientists are very good at that, so I think we just have to have a level mind here. This is an unusual time that is needing a very unusual solution.

“What we have to realise is, there’s no way we’re going to solve this problem by not involving industry. We’ve got to turn this ship around by going into the helm and working with all players, and if we have the right governance then I don’t think that the things people are fearful of will eventuate.”

Hoegh-Guldberg is also positive about scientific approaches to anything that could help get the reef through while the climate might be stabilised. “I think there’s some really serious interest in whether or not you can introduce gently, over decades, heat-tolerant corals, and the jury’s out on whether that’s going to work and we need to know whether that can be done,” he says.

“The normal way science would go would be, ideas would be bubbling to the surface, then PhDs would be done. Then scientists would eventually write papers and it would be maybe five to 10 years before you had ideas in place to design technical solutions and so on. We don’t have that time.”

The Great Barrier Reef Marine Park Authority’s Russell Reichelt also looked for a positive angle on the funding. He issued a press release saying it was a “game changer”. Alongside the $443.3 million going to the Great Barrier Reef Foundation, his authority is getting the balance of $42.7 million over the next six years for its joint field management program.

“This is a hugely positive outcome for the Great Barrier Reef and comes at a critical time after back-to-back mass coral bleaching triggered by the increasing pressure of global warming,” Reichelt said. “We’re delighted to continue working with the Great Barrier Reef Foundation as they explore the possibilities this funding provides, including opportunities to seek co-funding from investors to add to this investment.”

Significant questions remain about the Turnbull government’s motivations and its processes. The funding allocation remains deeply curious. Again we see the federal government outsourcing what would normally be the work of a government agency to a private body. It is likely the Great Barrier Reef Foundation will be spending its new-found money before we know why it was chosen to receive it. But for at least some of the scientists involved, that may be a good thing.