The Great Barrier Reef is still at risk of a widespread outbreak of coral bleaching despite a cyclone to the far west helping to temporarily cool stressed corals, according to US and Australian science agencies.

Clearer skies, weak tides and above-average ocean temperatures are combining to create stressful conditions for corals along much of the world’s largest reef system.

Concerns are rising that southern parts of the reef that escaped major bleaching in 2016 and 2017 may be hit in the coming weeks unless weather conditions change.

Australia’s marine science agency said on Thursday it was set to deploy a second underwater glider to monitor water temperatures in the central and southern areas of the reef.

Townsville-based Dr William Skirving, of the US government’s National Oceanic and Atmospheric Administration’s (Nooa) Coral Reef Watch, told Guardian Australia: “Everything seems to be lining up.

“The clouds are clearing and we can see the heat is still high and we know the tides will provide less and less mixing. Everything is falling in line for a short sharp bleaching event but the severity of it is difficult to predict.”

Corals bleach when they sit in abnormally warm water for too long. The algae that live in the corals and provide much of its nutrients and colour leave their host, leaving a visible white skeleton behind. Corals can recover from mild bleaching.

Coral reef systems have been long predicted to be susceptible to global warming. The United Nations science panel has said that even at global heating of 1.2C “most available evidence” showed that in the tropics “coral-dominated ecosystems will be non-existent at this temperature or higher”.

Dr Katharina Fabricius, a senior principal research scientist at the Australian Institute of Marine Science, said: “The reef is still on a knife edge. The future of the reef now seems to depend on flukes of the weather. That is a big concern.

“This is exactly what scientists have been predicting, with an increase in the frequency of bleaching events.”

Tropical Cyclone Esther crossed the coast in the Gulf of Carpentaria on Monday morning and while the eye of the cyclone was hundreds of kilometres west, the weather system dragged clouds over the reef, helping to cool temperatures slightly.

The Great Barrier Reef Marine Park Authority said late Thursday weather conditions over the next few weeks would “play a key role in determining outcomes for the Reef this summer”.

Coral bleaching has been occurring on parts of the reef where thermal stress has accumulated the most over summer.

The authority said in-shore reefs in the far north had already experienced “widespread bleaching affecting most coral types” but there had been minimal bleaching on outer reefs.

So far, only patchy and isolated bleaching had been reported over large parts of the reef, the authority said.

Great Barrier Reef Marine Park Authority chief scientist Dr David Wachenfeld reports on the status of heat stress and coral bleaching on the Great Barrier Reef on 27 February.

Skirving said: “The clouds helped because they cooled things off, but there’s still a lot of heat in the system. It’s hot enough for the corals to be accumulating stress.”

He said the mass bleaching event of 1998 across the reef had taken place over the course of just one week.

Weak tides for the next week meant there was less mixing of the warmer surface waters with deeper, cooler water.

Skirving said if Cyclone Esther had not formed, “it would be already bleaching up and down the reef”.

In updated analysis, compiled on Wednesday, Skirving wrote that Noaa’s tool for predicting heat stress on corals showed there was an 80% chance that most of the reef would experience some bleaching between 1 March and 8 March. For southern parts, the probability was even higher.

Bleaching at Magnetic Island, inshore GBR, Feb 26th 2020.

About 65% of colonies showing stress, with some quite unusual patterns in the bleaching at present.

Next 2 weeks will be critical in determining mortality schedules.

#coralbleaching2020 #GreatBarrierReef pic.twitter.com/Tz1vqfI40t — Dr Andy Lewis (@DrAndyLewis1) February 27, 2020

Dr Sophie Dove, an associate professor at the University of Queensland’s Coral Reef Ecosystems Lab, said it was important to differentiate mild bleaching from severe events, where corals appeared starkly white.

“If that whiteness persists then we are likely to see mortality,” she said, adding it was too early to say if the current conditions would have a serious impact on the reef.

The Australian Institute of Marine Science (Aims) has been monitoring satellite data, their own weather stations and a network of more than 170 electronic temperature loggers to check temperatures.

Craig Steinberg, an oceanographer at Aims, told Guardian Australia that two autonomous underwater gliders were being used to record water temperatures from the surface to a depth of 200 metres.

He said after a brief cooling period, “we are now back into a warming phase” in the southern parts of the reef.

Temperatures tend to peak on the reef in mid-March.

Prof Terry Hughes, director of the ARC Centre of Excellence for Coral Reef Studies at James Cook University, said southern parts of the reef had a greater number of coral species that were more susceptible to bleaching.

He said: “We are at the stage where there’s enough heat to cause widespread, mild bleaching now, and we have two weeks to go.”

Coral bleaching at Magnetic island, near Townsville, recorded during a dive on 17 February.

Fabricius said she had seen a bleaching event unfolding at Magnetic Island, near Townsville, over the past two weeks.

At a snorkel trail at Geoffrey Bay, hard coral species were partially bleached, giant clams were turning white and some acropora corals were showing signs of death.

“The forecast for Friday is for 35C with clear skies,” she added.