The federal government has unveiled its long term plan for the Great Barrier Reef, hoping to avert a United Nations declaration that the natural wonder is in danger.

The plan includes a ban on dumping dredge spoil anywhere in the world heritage area, a limit on port expansion to four sites and targets for reducing sediment, nutrient and pesticide contamination.

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At its launch on Hamilton Island on Saturday, Prime Minister Tony Abbott said the plan took reef protection to the next level, with improving water quality the absolute key.

He said pesticide, sedimentation and nitrogen run-off had all fallen since 2009.

“Under the long term sustainability plan driven by the extra $100 million we are putting into the reef trust, things will improve further and further,” he said.

Environment Minister Greg Hunt said an independent scientific panel led by Professor Ian Chubb would monitor and set priorities for improvement.

“The heart of this plan is about better quality, with hard targets including a 50 per cent reduction in nitrogen by 2018 and an 80 per cent reduction by 2025.”

Queensland Environment Minister Steven Miles said run-off of sediment, nutrients and pesticides was the biggest medium term threat to the reef, which the plan addressed.

“With it, we will be able to convince the World Heritage Committee that not only should they not list the reef as in-danger but that we will actually keep the reef from being in danger,” he said.

The World heritage Committee of UNESCO deferred a decision on the reef’s status last year and is due to make a draft decision in May before a final conference in June.

The Queensland Resources Council said the Reef 2050 Long Term Sustainability Plan was a landmark collaborative effort to protect the reef’s health for decades.

But Greenpeace called it a weak plan which still allowed massive coal port expansion and barely dealt with climate change, despite the government’s own scientists declaring this the number one threat.

Shadow environment minister Mark Butler said it was a vast improvement on the draft thanks to intervention of the new state Labor government.

He said Labor welcomed commitments to improving water quality but not the government’s proceeding with handing environmental protection powers to state and local governments.

“Labor believes the protection of the Great Barrier Reef should be the responsibility of the national government,” he said in a statement.

Queensland Greens senator Larissa Waters said the plan wouldn’t stop the reef becoming a coal ship super highway.

And while $100 million to stop run-off was welcome it was nowhere near enough.