The worst coral bleaching in the history of the Great Barrier Reef has already killed half the corals in reefs off the far north Queensland coast, the head of the reef's Marine Park Authority said.

Questions in Senate estimates on Thursday also revealed that the $171 million claimed by Environment Minister Greg Hunt earlier this week as a "boost" for the reef's protection came from other programs and was not "new money".

The authority noted the work done by scientists such as Professor Terry Hughes, whose survey team had found only 7 per cent of the Great Barrier Reef had not been affected by coral bleaching.

Russell Reichelt, the reef's Marine Park Authority chairman, told Senate estimates on Thursday that the region of the reef north of Lizard Island had been the worst hit, with "severe bleaching", although the event as a whole was "very widespread".

There is a "very high mortality in the far northern section" and was likely to be above 50 per cent of corals, Dr Reichelt said. The area was known as being relatively pristine.

Dr Reichelt noted that two of the big three bleaching events had occurred during an El Nino, such as this year, but climate change was "by far the biggest signal".

The bleaching is "driven by the upward trend in ocean temperatures, which is about 1 degree in the past century," he said. "It is very strongly linked to global warming."

Temperatures have lately been at record levels in the region, as noted by GBRMPA:

Another record month of temperatures on the #Reef confirmed by Bureau of Meteorology. Follows hottest Feb and March. pic.twitter.com/gbCD9KoK45— GBR Marine Park (@gbrmarinepark) May 5, 2016

Bleaching starts to affect corals when ocean temperatures exceed thresholds for about four weeks, Dr Reichelt said. At that point, corals expel algae, known as zooxanthellae, that live in their tissues and serve as their source of nutrients.

Some coral species start to die if those excessive temperatures continue for another month, although long-lived large boulder-like corals can survive to 12 weeks or longer after the threshold levels of warm waters are exceeded.

The bleaching was less widespread in southern reaches of the reef but became worse from about Port Douglas northwards, he said. Some of the reefs were also dying near Cairns but other reefs were faring better.

The Bureau of Meteorology is projecting that sea temperatures will remain above average for some months to come for much of the region. (See chart below.)

Dr Reichelt said water quality was the second-biggest threat to the reef, noting that nutrient levels entering the coastal fringing reefs were four to five times higher than the conditions corals had evolved in.

He praised efforts by governments to improve water quality as "a terrific national response".

Coral waters are relatively nutrient poor. A pulse of nutrients, such as after floods, boost the growth of green algae that compete with corals.

Old money

Answers from officials from the Environment Department and Education Minister Simon Birmingham also confirmed that the $171 million announced in this week's budget for reef funding came from raiding programs such as the National Landcare Program and capping spending on the Green Army.

Greens Senator Larissa Waters said the Turnbull government's reef funding was "not only inadequate but it comes at the expense of other environment programs".

"In a budget that keeps more than $20 billion in subsidies to fossil fuels and gives $100 million in new money to mining exploration, it's an indictment on the government that there is no new money for the reef that doesn't come at the expense of other environment programs," Senator Waters said in a statement.

"We are in an extinction and climate crisis – now is not the time for more environment funding cuts," she said.

On Tuesday, Mr Hunt said in a media statement: "The Turnbull Government is doing more than ever before to protect the Great Barrier Reef and the 2016 Budget strengthens this commitment with a $171.0 million boost".

Global attention

Professor Hughes' surveys drew global attention, including his social media comments.

I showed the results of aerial surveys of #bleaching on the #GreatBarrierReef to my students, And then we wept. pic.twitter.com/bry5cMmzdn— Terry Hughes (@ProfTerryHughes) April 19, 2016

Many other reefs around the world, including off north-western Australia, are also affected by bleaching as the El Nino leads to a spike in temperatures in many oceans against the background of warming seas from climate change.

Reefs around Christmas Island, such as Flying Fish Cove, were reporting bleaching of 70-75 per cent of corals in waters less than eight metres deep, and as as much as 30 per cent for corals in deeper waters, Jason Mundy, an Environment Department official, told Senate estimates.