The scientists from James Cook University in north Queensland criticised the government plan for ignoring climate change and not properly funding water quality improvement plans, among other issues.

Co-author Professor Terry Hughes said Australia could no longer afford to take a "business as usual" approach to the reef.

But he stressed the article, published in the journal Nature Climate Change, was about trying to fix problems with the reef rather than creating a sense of "doom and gloom".

"We're not setting out to be hyper critical," he said.

"We actually want to put the science to use and we certainly don't want to throw our arms up in the air and say it's all stuffed."

Professor Hughes is the director of the Australian Research Council Centre of Excellence for Coral Reef Study. (ARCCECFS)

He co-wrote the paper with Jon Brodie from the Centre for Tropical Water and Aquatic Ecosystems Research and Jon Day, also from the  ARCCECFS after a comprehensive study of the factors damaging  the reef.

The study found every major stressor on the reef - including increased  fishing, pollution, coastal development, dredging and  climate change - has been escalating for decades and will continue to increase two or three times over by 2050.

Prime Minister Tony Abbott and Environment Minister Greg Hunt last month launched the Reef 2050 Long-Term Sustainability Plan.

Mr Abbott also announced an extra $100 million for a long-term plan to protect the reef, which would go to landowners near the reef to improve water quality.

But the scientists argue more needs to be done, proposing a six-point plan to restore the reef.

1. Australia must take a leading role in tackling climate change and abandoning fossil fuels

The JCU researchers' biggest concern with the government's proposal to protect the reef is a lack of action on climate change.

The government admits climate change is the biggest threat to the reef and the scientists argue it needs to take more action to reduce emissions and reliance on fossil fuels.

"It (the plan) describes climate change as a global problem and a long term problem, with the inference that it can be postponed and it's not really Australia's responsibility and I don't think that's valid," Professor Hughes said.

"Climate change is already affecting the barrier reef.

"We've seen large-scale bleaching of corals from global warming going back to 1998.

"For marine biologists like myself, climate change is something we're measuring now it's not something that might happen in the long term."

A spokeswoman for Environment Minister Greg Hunt said the government was working on climate change domestically and internationally.

"Our $2.55 billion Emissions Reduction Fund will assist us in reaching our 2020 domestic target," she said.

"Internationally, we are working with the rest of the world in achieving a good outcome at the Paris conference at the end of the year for new targets post 2020."

The Emissions Reduction Fund and the government's climate change efforts has been condemned as ineffectual and inefficient.

2. Permanently ban all dumping of dredge spoil in the Great Barrier Reef World Heritage Area

The current plan bans "capital" dredge spoil dumping in the Great Barrier Reef Marine Park.

This leaves a coastal section unprotected but the Queensland government has promised to ban dumping in this in-shore area.

Professor Hughes' bigger concern is that the plan still allows for dredging to maintain existing channels, which he predicts will increase greatly in coming years.

"When you dump fine sediment it obviously disperses a long way, it doesn't sink like a stone," he said.

"Sediment smothers plants and animals, particularly juvenile corals, baby corals."

He said it could also make fish sick and kill off seagrass and coral because of reduced light, creating wider impacts for fish, sea turtles and dugong.

A spokeswoman for Mr Hunt said the government was taking action to minimise maintenance dredging but some was needed to "avoid an even greater environmental disaster" if ships ran aground.

3. Emphasise conservation and protection instead of sustainable development

The Great Barrier Reef Marine Park Act 1975 speaks about protection and conservation biodiversity but Professor Hughes argues the approach today is focused on allowing sustainable development, to the detriment of the reef.

"From a science perspective it seems extremely far fetched that you could actually have the world's biggest coal mines with the world's biggest coal ports immediately adjoining the Great Barrier Reef World Heritage Area," he said.

"We can either have a healthy barrier reef without the Galilee Basin or we can have the Galilee Basin but we can't have both."

4. Overhaul environmental impact assessment process

Companies have to go through long and involved environmental impact processes before they get the green light for projects in the reef's catchment area.

But Professor Hughes says the process is flawed because the company itself completes the assessment, rather than an independent body, and they typically produce documents with hundreds of pages that can't be properly interpreted in the time allowed for public feedback.

He also has issues with the concept of offsetting environmental damage with financial donations towards other environmental projects, with the aim of creating a net benefit to the environment.

"There's a whole slew of problems with offsets," Professor Hughes said.

"The 2050 plan will be largely funded by that kind of funding.

"So it sets off a fairly perverse dynamic where the more damage you allow to the reef the more money there is available to protect it and we just think that's a recipe for disaster."

5. Make the Great Barrier Reef Marine Park Authority (GBRMPA) responsible for all aspects of the reef again, including fishing and ports

The Great Reef Marine Park Authority had its budget slashed by $2 million last year amid cuts to the federal Department of Environment budget. The JCU researchers' plan recommends the authority's funding be restored and it be put in charge of fishing and ports.

"They lost a lot of expertise in areas like climate change, fishing, water quality and they really need the expertise within the agency to do their job," he said.

6. A 50-year plan and funding for use of the catchment inland of the reef

Professor Hughes says the government's 2050 plan for reef management ignores a critical component, what happens on the land that feeds into the reef marine park.

The catchment area is almost twice the size of Italy and what's done on land can have huge impacts on the health of the water.

"Moving forward we really need to think about how all that land area is used in terms of what that'll mean for runoff of sediment and nutrients and for CO2 emissions," he said.

"At the moment we have a $10 billion plan for the Murray-Darling Basin but we don't have any plan and almost no money for the future of the barrier reef."

A spokeswoman for Mr Hunt said federal and Queensland government investment in reef protection was projected to be more than $2 billion dollars over the next decade, including the $100 million committed to the Reef Trust last month.