There are concerns the northern third of the Great Barrier Reef could be permanently damaged if a weather event causing coral bleaching does not subside.

Hot summer conditions and rising water temperatures have already led to major coral bleaching and death.

The concerns come despite scientists previously believing a major coral bleaching event had been avoided.

Last year, the United Nations spared the Great Barrier Reef from being declared "in danger" for reasons including climate change.

But the reef has not been so lucky this summer.

A research centre in Queensland's Far North is now warning a significant part of the UN world heritage site could disappear from steady high water temperatures and strong sun exposure.

The director of the Lizard Island Research Station, Dr Lyle Vail, says the reef's northern third is almost completely bleached.

"The coral bleaching, especially in the shallow lagoon areas, is actually quite severe. About three weeks ago or so, about half the corals had some levels of stress. Now, it's ramped up to most of the corals are quite severely distresssed, and that means that they're pure white in colour. And even some of them are starting to die."

A lull in the El Nino's hot, dry conditions and high sea surface temperatures had given scientists hope the worst coral bleaching event in over a decade had been averted.

But reports from scientists on the reef have prompted the Great Barrier Reef Marine Park Authority to increase the coral bleaching threat level.

The director of reef recovery, David Wachenfeld, says the change in weather forecast has come as a shock for the reef.

"Right since the beginning of December, we have known that this was a high risk year for the Great Barrier Reef. Now we've seen in December and January some good weather that did not lead to heat stress, but then all got turned around in February, which was really a shocker for the Great Barrier Reef. And we've, regrettably, seen a number of reefs were there is now severe bleaching, which is probably not surprising given the heat stress that those reefs have seen. But this means that large proportions of the coral are bleaching, and they're bleaching absolutely bone white. It's not just paling, it's not just mild stress, it's severe stress."

The reef authority sent out research boats last month to areas of the reef more susceptible to bleaching.

What they found was worst than expected.

The bleaching threat is at Level 2, but Mr Wachenfeld says it is likely to increase to the third, and last, level.

"The stress from the heat is not going away for the corals. I think it is perfectly possible that, as this event continues to evolve, we may see that we have to raise our response level to response level 3."

If water temperatures return to normal, bleached corals can regain their colour.

But they rarely fully recover and are more likely to bleach again.

Persistent, extreme water temperatures that last for eight weeks or longer can often make coral starve and eventually die.

In 2002, 60 per cent of the almost 3,000 individual reefs that stretch over an area about the size of Italy were bleached.

Reef authorities says at least half of the corals have already been lost.

Australian Institute for Marine Sciences researcher Dr Neal Cantin says a temperature increase of just one or two degrees causes bleaching.

"Coral bleaching is a stress response of the animal coral host to severe temperature stress in combination with light exposure, so, when the oceans calm down during the summer, we have low wind conditions, low cloud cover, high light, this heats the surface of the ocean. The surface of the ocean then warms the water column. And when corals experience temperatures one or two degrees above typical summertime conditions, the coral suffers stress from the algae symbiont that live within the tissue, and coral bleaching is basically the coral host getting rid of this algae symbiont, and you can see through the clear tissue to their white limestone skeleton."

Scientists across Queensland will continue to monitor corals and reef water temperatures.

But Professor Vail says he has no doubt some corals are dead and more could be lost.

"The mortality rate of the corals around Lizard at this point is pretty low, way less probably than 5 per cent. However, what we're afraid of is that, if these stress conditions get quite prolonged for another couple of weeks or so, then the number of corals that die will obviously increase."

Marine Park Authority researchers simulated the effects of coral bleaching events occurring once per decade 200 years into the future.

They predict significantly degraded reefs by 2100.

The director of James Cook University's Centre of Excellence for coral reef studies, Professor Terry Hughes, says such events will continue if greenhouse gas emissions are not cut.

"This is the third bleaching event we've seen on the reef. The frequency of these large-scale bleaching events is increasing worldwide as global temperatures continue to climb. We've now got to the unfortunate position where, every time we have a hot summer, there's a strong likelihood of seeing some bleaching. We really need to deal with the root cause of that, which of course is global emissions."