The storm caused widespread destruction when it hit Australia's northeastern coast and the damage would extend below the waves, said David Wachenseld, director for science at the Great Barrier Reef Marine Park Authority, on Monday.
In the area covered by the centre of the storm, "you're looking at the death of almost all corals on parts of the reef that were affected by the wind and the waves." he told AFP.
"All hard corals and things like sponges, soft corals, sea fans -all this kind of thing - live, stuck to the sea floor just like a tree, is rooted in one place, so they just have to sit there and take the brunt of it.
"Most of the bigger animals you'd expect would have swum away and wouldn't really have been affected," Wachenseld said.
While there had no been time to physically check the damage, Wachenseld said he based his assessment on the destruction caused by Cyclone Ingrid last year.
That storm caused little damage when it came ashore in a sparsely populated part of the coast, but damaged coral over a 160km wide path, with destruction highest in the centre.
"The important thing is that the Great Barrier Reef is one of the healthiest coral reefs in the world"
Director for Science,
Great Barrier Reef Marine Park Authority
"To put that in perspective, the reef is more than 2000 km long," Wachenseld said.
In areas of minor damage "you won't notice a difference in a couple of years, but in the middle where most and even all corals are killed, you're probably looking at 10 to 20 years for a recovery.
"The important thing is that the Great Barrier Reef is one of the healthiest coral reefs in the world.
"Humans can't go and fix the damage caused by a cyclone but humans can make the difference between whether or not a coral reef system is healthy enough to fix itself - and the Great Barrier Reef many times before has demonstrated to us that it is healthy enough to do that."
The Great Barrier Reef is the world's biggest coral system, stretching over more than 345,000 sq km off Queensland's coast. The marine park has been listed by the United Nations as a World Heritage site.
It is a main feature of Australia's multi-billion dollar annual tourism industry.