Four environmental groups have written to the UN environmental arm, UNESCO, accusing the government of breaking promises made when the Great Barrier Reef was at risk of being listed as a World Heritage site "in danger".

The Australian Conservation Foundation, Australian Marine Conservation Society, WWF Australia and Wilderness Society say 36,600 hectares of old-growth forest have been earmarked to be bulldozed in reef catchments.

Permits were granted under Queensland's former LNP government and while the now-state Labor government has tightened the laws, existing permits can't be cancelled.

The groups argue the federal government could intervene.

"Australia's promise to strengthen laws to protect bushland in reef catchments was one of the key pledges that convinced the World Heritage Committee not to place the reef on the in-danger list in 2015," AMCS reef campaign director Imogen Zethoven said on Monday.

"While Queensland recently passed stronger laws, the federal government has so far failed to use national environmental law to stop large-scale tree clearing in the reef catchment to help fulfil this critical promise."

The groups wrote the letter to coincide with the UNESCO World Heritage Committee annual meeting in Bahrain.

Federal Environment Minister Josh Frydenberg said the government's reef policy had been well received by the UN.

"The $2 billion Reef 2050 Plan has received significant praise from the United Nation's World Heritage Committee and led to the reef being taken off the in-danger watch list," Mr Frydenberg told AAP.

He said land clearing was primarily the responsibility of state governments.

Land clearing can affect reef health in two ways.

Runoff from denuded land carries more sediment out to sea, where it can settle on reefs and block the light corals need to survive.

Runoff from cleared land can also carry higher loads of nutrients to the reef, fuelling algal growth and outbreaks of crown-of-thorns starfish.

Australian Associated Press