The project will aim improve water quality, target coral-eating crown-of-thorns starfish (COTS) and implement scientific reef restoration of the reef.
"We have seen right across the world a number of reefs being hit by this heat stress and this is combined here in Australia with also Cyclone Debbie as well as the Crown-of-thorns starfish", he said.
However, Foreign Minister Julie Bishop said that Australia was a world leader in managing and protecting its reef, as the government's Reef 2050 plan had been approved by the UNESCO World Heritage Committee as being the standard for the rest of the world to follow.
"We'll be improving the monitoring of the reef's health and the measurement of its impacts", he said from Cairns in Far North Queensland.
Investigations showed that two successive heat waves killed almost half of the corals in the most pristine part of the Great Barrier Reef.
"The Turnbull Government will invest more than $500 million - the largest ever single investment - to protect the reef, secure its viability and the 64,000 jobs that rely on the Reef", Frydenberg said.
Mr Frydenberg said despite coral bleaching events in recent years, the Great Barrier Reef was "remarkably resilient" and it was important for the world to know that. "You can't have both", Ms Casule said in a Greenpeace statement on Sunday.
The Great Barrier Reef Marine Park Authority and The Department of the Environment and Energy will also get an additional funding of $56 million.
The bulk of the new funding - just over $151 million - was earmarked to improve water quality by changing farming practices and adopting new technologies and land management.
The government, in a partnership with the Great Barrier Reef Foundation, will contribute $444 million.
The federal government of Australia is allocating half a billion dollars to save the Great Barrier Reef from climate change and other threats.
In 2016, Labor also pledged $500 million of funding over five years towards the Reef if elected.