The agency said more bleaching was being observed in the central part of the reef, which past year escaped widespread severe bleaching.
The unusually high temperatures of the water are affecting the population of corals.
The back-to-back bleaching is also an indication that the coral is losing its ability to recover from extreme heat, Neal Cantin from the Australian Institute of Marine Science said in the release.
When sea surface temperatures rise, corals expel the colourful algae.
"As we saw a year ago bleaching and mortality can be highly variable across the 344,000 square kilometre Marine Park - an area bigger than Italy", he said.
Coral can survive for a while after bleaching, but generally die off within about two months.
Australia hasn't done almost enough to protect its most valuable national treasure, the Great Barrier Reef, according to environmental advocates.
Hughes, who begins his own aerial survey of the reef next week, warns that as bleaching events occur more frequently, affected corals will never be given a chance to fully recover, putting the reef in severe danger. The bleaching is the result of 12 months of above-average sea temperatures, which is "cooking the reef alive".
"We can't afford to sit by and watch climate change drive all the world's coral reefs to extinctions by the end of the century", Julia Baum, a reef researcher at the University of Victoria, told Climate Central previous year. This followed severe bleaching along the 1,500-mile stretch of reefs past year - the worst on record - caused by warm sea temperatures in March and April.
"There is no doubt that if we do not get our act together globally we will have serious damage to the barrier reef, we could see the barrier reef lose a huge amount of biodiversity, when you look at the Cayman islands they have about 30 species of coral and we have 300". "If this is the new normal, we're in trouble".
'We are extremely concerned moving into the future'. If oceans warm 2.7°F, it will essentially be a death sentence for most coral.
Dr Cantin said the "extent and severity" of this year's bleaching would not be known for another month.
"While the reef is fighting for its life, the Australian government is funding its destruction".
"The Palaszczuk Government has committed an additional $100 million over five years to protect the Great Barrier Reef", he said.
Environmental groups are acting against the proposed construction of the largest coal mine in Australia, which could significantly contribute to the greenhouse gas emissions.
Bleaching happens when warm waters cause the coral to oust algae living in their tissues.