The accounting move - dubbed by some as profiling - improved the outlook for coming years, including the government's promise of delivering a modest surplus in 2019-20.

The one-off spending contrasts with Ms Marsden's expectation that her group's funding would be spread over six years. That would still be enough to swell it to a $70 million-a-year organisation, "which may make us the largest environmental NGO in Australia", she said.

Environment and Energy Minister Josh Frydenberg said the potential for a partnership with the group was discussed "earlier this year".

"Both the Great Barrier Reef Foundation and the government are satisfied that [the group] will be able to scale up their operating model to deliver the investment," he said.

The government's choice surprised many, not least because the foundation will be the main funnel for money to more established bodies, such as the CSIRO, Australian Institute of Marine Science and the reef's own Marine Park Authority.

"If your only priority was delivering work on the ground to protect the reef, you’d have the department manage it directly," Labor's environment spokesman Tony Burke said.

The government's failure to address climate change  - which the foundation itself recognises as the reef's biggest threat - was a key element missing in the rescue plan.

"It’s like turning up to a natural disaster with a packet of Band-Aids," Mr Burke said.

One scientist who asked not to be named, said: "Obviously this is political - it's to head off Labor making a big issue of the Great Barrier Reef at the next election."

The Greens' environment spokesman Andrew Bartlett said there were "a number of significant questions that must be fully answered about how this amount of money will be managed and spent, as well as the contrasting issue of identifying the true impact of budget and staff cuts in the environment department".

Some mystery shrouds the foundation. Ms Marsden - who is married to Ben Myers, chief of staff to former Queensland premier Campbell Newman - declined to name the four "small businessman" who founded the organisation in 2000 after a chance meeting at Sydney Airport.

Fairfax Media understands one of the four is John Schubert, the foundation's current chairman and a former chairman of both Esso Australia and the Commonwealth Bank.

Ms Marsden dismissed speculation that another of the four was the late Sir Ian McFarlane, a Queensland shale oil developer.

The chairman's panel lists about 55 organisations "all with an interest in, and commitment to, the Reef".

These include coalminer Peabody Energy, gas developer ConocoPhillips and Qantas.

Invitation-only membership carries an annual donation of between $10,000 and $50,000, Ms Marsden said, declining to be more specific.

Ove Hoegh-Guldberg, director of the University of Queensland's Global Change Institute and a noted coral reef scientist, defended the foundation and the sum involved, saying: "It might sound like an enormous amount of money, but the problem is huge."

Professor Hoegh-Guldberg, who has served on the foundation's international scientific advisory committee since its inception, said the group's corporate membership was its strength, bringing management nous as well as the ability to leverage further philanthropy.

"This is a problem that transcends science," he said. " It's an all-hands-on-deck moment."

Still, several scientists told Fairfax Media they had concerns about the group's ability to graduate from a body now playing a mostly gap-filling role.