It could be a decade before the southern Great Barrier Reef recovers from the destruction caused by Cyclone Debbie, scientists have said.
Angus Thompson, from the Australian Institute of Marine Science (AIMS), said the damage was striking.
"Some of the reefs have had a substantial loss of coral cover — in excess of 95 per cent of the coral gone," he said.
Mr Thompson heads the inshore reef monitoring program that feeds into the annual Great Barrier Reef Report Card.
The yearly assessment details the progress of the Australian and Queensland governments' Reef 2050 plan.
His team has just finished this year's assessment of the Whitsunday Islands region, the first since the area was smashed by Cyclone Debbie in late March.
When the category-four system struck the Whitsundays off north Queensland, it was driving 260 kilometre per hour winds that battered the region and the reef from Mackay to Bowen for 48 hours.
"We have had big disturbances, but often not at this sort of magnitude from cyclones before," he said.
Seven checked reefs had damage to 95pc of coral
Each year, the scientists film and photograph at the same spots.
The 2017 photos are in stark contrast to photographs of the same locations taken three years ago.
Heavy sediment sits thickly over the wrecked coral and clouds the water, with no sign of the previous healthy reef.
"In the shallow waters, 60 to 70 per cent of the substrate was covered in branching, fast-growing corals that have been completely removed at some sites down to virtually nothing," he said.
"Down deeper, the corals have been more turned over and rolled around and so there are still small parts of those corals surviving, but there's big furrows down through it where material has just wiped down the slope and taken everything in its path.
"To reach the coral cover that we had prior to this, is a decade for most of these reefs."
Mr Thompson said his team checked seven reefs and most had damage to more than 95 per cent of the coral.
Only one was not badly impacted with damage to 10 per cent of the coral.
Not clear how far damage reached
Great Barrier Reef Marine Park Authority (GBRMPA) spokesman Mark Read said it was not clear how far the damage extended.
"But we do know the path of the cyclone was at least several hundred kilometres wide and depending on the area, the severity of the winds and the waves, were quite damaging," he said.
"When we get a tropical cyclone rolling across the reef, we do get extensive damage to live corals and certainly one of the things that is of concern is the capacity of that reef to bounce back after the impact."
Less coral means less breeding stock and that will slow recovery for the southern part of the reef, which had avoided the impact of increased sea temperatures in the north.
"Unfortunately, it came on top of the second consecutive mass bleaching event for the Great Barrier Reef," Mr Read said.
He said cyclones and increased sea temperatures were the biggest threat to the reef, which could only be tackled through long-term programs aimed at improving water quality, reducing land run-off, and cutting down greenhouse gases.
The GBRMPA will manage the impacts and recovery work going forward, but said there was good news for tourists, and scientists agreed.
Mr Thompson said coral recovery work began immediately after the cyclone, and included turning coral back over and returning to coral reefs, which means there are still beautiful dive spots for tourists.