Great Barrier Reef Foundation managing director Anna Marsden said the work was helping restore the island's critical habitat.
Stunning footage has captured up to 64,000 turtles bobbing about in the ocean together.
Researchers at Raine Island, the world's largest green turtle rookery on the Great Barrier Reef, used a drone to count how many green turtles were in the area.
The vision, captured last December, shows the turtles waiting to come ashore and lay clutches of eggs.
Dr Andrew Dunstan, from Australia's Department of Environment and Science, said researchers had been investigating different ways to count turtles.
"Previous population survey methods involved painting a white stripe down the green turtles' shell when they were nesting on the beach," he said.
"The paint is non-toxic and washes off in a couple of days.
"From a small boat, we then counted painted and non-painted turtles, but eyes are attracted much more to a turtle with a bright white stripe than an unpainted turtle, resulting in biased counts and reduced accuracy."
Dunstan said trying to accurately count thousands of painted and unpainted turtles from a small boat in rough weather was difficult.
"Using a drone is easier, safer, much more accurate, and the data can be immediately and permanently stored," he said.
Researchers analysed the footage frame by frame to make sure counts were correct.
Research partner Richard Fitzpatrick, from the Biopixel Oceans Foundation, said when they compared drone counts with boat counts they found they had underestimated the numbers in the past by a factor of 1.73.
"By using drones we have adjusted historical data," he said.
"What previously took a number of researchers a long time can now be done by one drone operator in under an hour."
Great Barrier Reef Foundation managing director Anna Marsden said the work was helping restore the island's critical habitat.
"We're seeing the world's largest aggregation of green turtles captured in these extraordinary drone images that are helping to document the largest turtle numbers seen since we began the Raine Island Recovery Project," Marsden said.
"This important research combines science and technology to more effectively count endangered green turtles.
"We're taking action to improve and rebuild the island's nesting beaches and building fences to prevent turtle deaths, all working to strengthen the island's resilience and ensure the survival of our northern green turtles and many other species."
In the future researchers hope to automate the counts from video footage using artificial intelligence so the computer does the counting for them.
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