The Australian government’s multimillion dollar plan to halt the worrying decline of the Great Barrier Reef does nothing to address the leading threat of climate change and is likely to prove largely ineffectual, scientists have warned.

In its formal response to the Reef 2050 long-term sustainability plan, which was drawn up by the Australian and Queensland governments, the Australian Academy of Science states the strategy is “inadequate to achieve the goal of restoring or even maintaining the diminished outstanding universal value of the reef”.

Although a recent government assessment found climate change is the leading threat to a declining reef, the Australian Academy of Science states there is “no adequate recognition” in the 2050 plan of the importance of curbing greenhouse gases.

The academy’s submission is also critical of what it sees as the plan’s lack of specific funded goals to restore the reef’s condition, along with a failure to properly tackle issues such as poor water quality, coastal development and illegal fishing.

“The draft 2050 plan represents business-as-usual in terms of how escalating pressures on the reef are adequately regulated [or not], when much bolder action is required to restore the values of the reef and prevent further degradation,” the submission states.

Professor Terry Hughes, director of the Australian Research Council Centre of Excellence for Coral Reef Studies and an academy fellow, said the plan was focused on the sustainable development of four “mega ports” adjacent to the reef, rather than conservation of the reef itself.

“There’s no questioning in the report of whether two or three ports would be better than four,” Hughes told Guardian Australia.

Ports such as Abbot Point, near the Queensland town of Bowen, are being expanded to allow for larger exports of fossil fuels.

“There’s nothing in the plan on addressing climate change,” Hughes said. “The science is quite clear that you can’t keep the Great Barrier Reef in good condition if you’re going to develop huge coal reserves. We are already on our way to 2C warming and unless Australia cuts back on carbon dioxide emissions we won’t have much of a Great Barrier Reef left.

“We need a plan to transition away from fossil fuels well before 2050. Australia’s emissions reduction goal is very, very weak by international standards. We have stewardship of one of the world’s premier reef systems and also stewardship of a huge reserve of fossil fuels – it’s a conflict of interest, really.”

Key threats to the reef, aside from climate change, include pollution flowing onto the ecosystem from agriculture, cyclones and a plague of coral-eating starfish. The reef has lost around half its coral cover in the past 30 years.

The Reef 2050 plan sets a target of a 50% reduction in nitrogen and a 60% drop in pesticides flowing onto the reef by 2018. There is also a plan to protect dugongs and turtles. However, there is no new funding mentioned beyond the $40m Reef Trust program announced in the budget.

The plan includes no specific ban on the dumping of dredged seabed spoil into the reef’s waters, which scientists say can smother and badly damage coral and fish. A proposal to dump dredged spoil into the Great Barrier Reef marine park for the Abbot Point project was recently reversed, although a similar dumping plan is in place to facilitate the expansion of other areas, such as the Townsville port.

“The proposed dredging is unprecedented and will swamp the reef,” Hughes said.

“The government has spent around $400m on reducing by about 10% the amount of sediment flowing out onto the reef but this is completely overtaken by the amount of sediment being dumped.

“There are literally hundreds of reports saying mud dumped on your head isn’t good for you. It isn’t really rocket science. The government needs to engage with scientists more than they did when putting together this draft plan.”

Unesco’s world heritage committee will decide next year whether to place the Great Barrier Reef on its “in-danger” list. Unesco has called for port expansion to be limited in order to safeguard the health of the reef.

“There’s no doubt the short-term goal of this report is to keep Unesco happy,” Hughes said. “I’m not sure if that will succeed or not but in terms of this being a plan for the next 35 years, there are missing targets that need to be in there.

“It would be a terrible outcome if the Great Barrier Reef is placed on the in-danger list; it would be very damaging to Australia’s reputation. I haven’t met anyone who wants that to be the case but I wouldn’t be surprised if Unesco went ahead and did it.”

On Monday, Greg Hunt, the federal environment minister, unveiled new guidelines to increase the number of divers able to lethally inject crown-of-thorns starfish, which are munching their way through the reef’s coral.

A spokesman for Hunt said the 2050 reef plan is based on the “best available science to ensure it responds to new and emerging issues”.

“We have a clear plan and a strong commitment to ensure the reef is healthy and resilient – and we are making strong progress,” he said.

“The Great Barrier Reef remains an incredibly diverse and rich marine environment. We know the reef still retains the values for which it was listed as world heritage.

“The Australian and Queensland governments are jointly investing approximately $180m a year in the reef’s health – that’s billions of dollars over the next decade.”