The experts from James Cook University (JCU) say it is the most extreme case of mass bleaching they have ever measured at the World Heritage Site.
Bleaching occurs when warmer water causes coral to weaken and lose the colourful algae that provide oxygen and nutrients.
It has been linked to climate change.
"We found on average, that 35% of the corals are now dead or dying on 84 reefs that we surveyed along the northern and central sections of the Great Barrier Reef, between Townsville and Papua New Guinea," Professor Terry Hughes, the head of the ARC Centre of Excellence for Coral Reef Studies at JCU, said in a statement.
"This year is the third time in 18 years that the Great Barrier Reef has experienced mass bleaching due to global warming, and the current event is much more extreme than we've measured before.
"We're rapidly running out of time to reduce greenhouse gas emissions."
The scientists warned that the recovery of coral cover is expected to take a decade or longer, but it would take much longer to regain the largest and oldest corals that have died.
Their study was released after months of intensive aerial and underwater surveys.
At least 35% of corals in the northern and central parts of Australia's Great Barrier Reef have been destroyed by bleaching, Australian scientists say.