The full impact of coral bleaching across the Great Barrier Reef will become clearer this week as aerial surveys of hundreds of reefs are completed in the bottom two thirds of the world’s biggest reef system.

An aerial survey carried out last week over almost 500 individual reefs between the Torres Strait and Cairns revealed some severe bleaching of corals closer to shore, but almost none on outer reefs.

From Monday the spotter plane will head south over reefs where satellite observations and temperature readings have shown corals are likely to have undergone higher levels of heat stress than those in the north.

Scientists fear those corals could be found to have been badly bleached, as they are less used to higher temperatures and had escaped major impacts in 2016 and 2017.

The chief scientist at the Great Barrier Reef Marine Park Authority, Dave Wachenfeld, told Guardian Australia that whatever the survey concluded, the current bleaching should sound “a very loud alarm bell” on the plight of the reef under global heating.

Heat stress has been building across the length of the reef this summer with many anecdotal reports from tourism operators, tourists and recreational diver of severe bleaching.

Day 4: We have now completed assessment of #coral bleaching between Cairns and northern Torres Strait.



Today, we saw extreme levels of bleaching on coastal reefs from Lockhart River to Cairns. Mid-shelf reefs in this region have variable levels of bleaching, from mild to severe pic.twitter.com/QdN16S0cV3 — Terry Hughes (@ProfTerryHughes) March 20, 2020

In February, average sea surface temperatures on the reef were 1.25C above normal and the highest on record going back to 1900. Scientists have said the world’s oceans are gathering heat due to accumulating levels of greenhouse gases in the atmosphere, mostly from burning fossil fuels.

Corals bleach if they sit in unusually hot water for too long. Survival from bleaching depends on how high and for how long temperatures get. Some species of corals have higher tolerance for heat than others.

Observations of conditions on the reef from satellites and in-water temperature loggers suggest central and southern parts have accumulated high levels of hat stress.

But the authority said the full picture would only come clear once the aerial surveys were completed at the end of this week, and the data had been analysed.

In 2016 and 2017, the world heritage reef experienced back to-back bleaching that was intense enough to kill almost half the reef’s corals over those two years.

Central and southern parts of the reef were not severely impacted in those years, meaning they are not used to the heat stress and could be harder hit.

Prof Terry Hughes, director of the ARC Centre of Excellence for Coral Reef Studies at James Cook University, spent 17 hours across four days in the air last week scoring bleaching on reefs with a staff member from the authority.

After completing the first four of nine days of aerial surveys, Hughes told Guardian Australia most of the severe bleaching had been seen at coastal reefs.

On Friday, flying from Lockhart River to Cairns, Hughes said corals at Princess Charlotte Bay at the bottom of the Cape York Peninsula had been severely bleached, but the impacts were much less on reefs further away from the coast.

Many of the outer reefs in the north – known as “ribbon reefs” because of their slim and snaking appearance from above – had escaped bleaching.

Hughes said: “A lot of the reefs we have been looking at were badly affected in 2016 and 2017. They don’t have a lot of corals on them and the corals that are there have managed to survive 2016 and 2017, and so they are tough.”

Hughes said it “remains to be seen what will happen in the south” but there were more coral species in those areas – including staghorn and table acroporas – that would be more susceptible to bleaching.

Some of those central and southern reefs “have accumulated a lot of heat, particularly near the coast,” he said. “This is shaping up to be strongly coastal – 2016 and 2017 were cooler in the south and, this time around, it is not cool in the south.”

Hughes said: “Even if it turns out to be a relative moderate event event compared to 16 and 17, it is still cumulative and because the footprints are different, the cumulative amounts of the reef that’s affected severely or moderately will go up.”

Townsville-based Dr William Skirving, of the US government’s Coral Reef Watch program at the National Oceanic and Atmospheric Administration, said the agency’s analysis showed how localised the heat stress had been. But whether that heat stress had translated to severe bleaching would be be answered by the aerial surveys.

He said according to his agency’s analysis, one area of Swains Reefs off Townsville had showed some of the highest levels of heat stress across the entire reef, but some of the lowest levels had also been in the same group.

This was one reason, he said, why the aerial surveys were important. He held concerns for the corals in southern areas.

He said: “Let’s cross our fingers that the corals were not as susceptible as they were in the past.”

Wachenfeld told Guardian Australia that whatever the final assessment was “these are still significant events that are sounding a very loud alarm bell about what’s happening to the reef in the face of climate change.”

He said there had been reports of “at least moderate bleaching” from Magnetic Island, near Townsville, and Heron Island, off Gladstone.

“Bleaching does not necessarily mean death and that some people do misunderstand that,” he said. “Yes, the reef is in trouble, but what that means is that it needs more help.”

Aerial surveys this week of the Ribbon Reefs, above Cairns, show little to no bleaching. Aerial surveys continue over the coming days in areas that experienced more heat stress. #GreatBarrierReef #video pic.twitter.com/4cdjpbj4ZE — Great Barrier Reef Marine Park Authority (@gbrmarinepark) March 20, 2020

Wachenfeld said whatever the final detailed assessment of the severity of this summer’s bleaching revealed, this needed to be seen in the context of the broader challenges the reef was facing, including the ongoing impacts from climate change.

He said 2016 and 2017 were “the worst events that have ever happened” for the reef, and so if this year turned out to be less severe, this should “not lull us into a false sense of security”.

He said he was encouraged to hear that outer ribbon reefs in the north – which he had personally dived on many times – had seemingly escaped bleaching this summer.

“They are some of the most beautiful places on the planet and so to know they have done well in this event gives me enormous hope for the future and of what we have left to protect,” he said.

“There are still places that are absolutely amazing. The reef as a whole is still a gobsmackingly amazing and beautiful place and it needs us to do more globally to protect it.”