Widespread coral bleaching is forecast for waters off the Northern Australia coast, due to above-average sea surface temperatures that could last for up to two months.

Key points: Average sea surface temperatures could hit 33 degrees Celsius for up to eight weeks

Average sea surface temperatures could hit 33 degrees Celsius for up to eight weeks A red alert for coral bleaching has been issued for most of the NT coastline

A red alert for coral bleaching has been issued for most of the NT coastline Cyclone systems could have a cooling effect on the sea surface temperature

Rising sea surface temperatures prompted the National Oceanic and Atmospheric Administration, part of the US Department of Commerce, to issue a "Red Alert Level 1" for coral bleaching off most of the Northern Territory coastline, apart from the Gulf of Carpentaria.

North of the Tiwi Islands, where sea surface temperatures have topped 33 degrees Celsius, a "Red Alert Level 2" has been put in place.

The administration said that meant there was a 60 per cent chance of mass coral bleaching across those areas.

It has forecast that all of the Territory's coastal waters, apart from parts of the Gulf of Carpentaria, will be on "Red Alert Level 2" by January.

"It looks like a large mass of really hot water is coming down through Indonesia, and it's going to sit above the Northern Territory and Kimberley Coast," the Australian Marine Conservation Society's northern campaigner Jason Fowler said.

"The administration is predicting we will have at least eight weeks of above-average sea surface temperatures over 33 degrees, so this bleaching event could last some time."

The NOAA coral bleaching alert area and outlook for the Northern Territory over the next 12 weeks ( Supplied: NOAA Satellite and Information Service )

The administration correctly predicted there would be coral bleaching off the Territory coast, including near the Cobourg Peninsula, earlier this year and in 2016.

In 2016, reefs off Arnhem Land and some parts of the Gulf of Carpentaria were bleached, and there was a mass die-off of mangroves stretching from Borroloola to Queensland.

'We expect just as bad, if not worse coral bleaching'

In the same year, sand temperatures on Bare Sand Island — a key flatback turtle nesting area — were so high, all of the hatchlings were incubated as females, and no males were born.

"In 2016 we saw widespread bleaching and the conditions predicted now are just as bad, so we expect just as bad, if not worse coral bleaching," Mr Fowler said.

Jason Fowler said cyclone systems could have a cooling effect on the sea surface temperature ( ABC News: Jane Bardon )

He said cyclone systems could have a cooling effect on the sea surface temperature, but when reefs bleached during years in close succession, it was more difficult for corals to recover and recolonise dead areas.

Mr Fowler has called on both the Northern Territory and Federal Governments to increase efforts to reduce carbon emissions to try and slow ocean warming.

"The Northern Territory seafood industry and coastal communities are at risk from this, so we really need to get on with reducing emissions," he said.

"And we need to get scientists out to the reefs to start studying the impacts."

Mr Fowler said he hoped the Northern Territory Government's forthcoming Coastal and Marine Management Strategy would contain measures designed to reduce other stresses on the Territory's coral reefs.

A red alert for coral bleaching has been issued for most of the NT coastline ( ABC News: Jane Bardon )

"We need to regulate fishing pressure, make sure reefs are not stressed by industrial developments," he said.

"And to make sure our rivers are flowing freely and unpolluted into the sea to help reefs function and recover from bleaching events as best as possible."

The Government has said it expects to release its Coastal and Marine Management Strategy next year.