It is hoped the project will help researchers collect data from the key breeding ground of remote Raine Island, where tens of thousands nest each year.
Their breeding rate on the island is a very low 20 per cent, well under the sustainable rate of 85 per cent.
The drones have been deployed to help researchers count the turtles and allow for more efficient and accurate data collection than counting from the ground.
The footage is also being used to monitor habitat loss, and areas of erosion on the island, which is about 620 kilometres north-east of Cairns and inaccessible to the public.
Dr Andrew Dunstan, manager of the Raine Island Turtle Recovery Project, hoped to stabilise the turtle population.
“If we don’t do anything now, then we would expect green turtle numbers to decline radically over the next two decades,” said Dunstan.
“So, one in five turtles that comes up on any night nest successfully, and the others have to come back night after night until they actually do,” said Dunstan.
“The new data from the drones gives us a great idea of what is happening, what are the changes going on to that turtle nesting beach area.”
Researchers have been reshaping parts of the beach to protect breeding grounds.
They said it has been a success, but will use the data from the drones to plan their next steps.
Anna Marsden, CEO of the Great Barrier Reef Foundation, praised the innovative nature of the project.
“It’s a positive step that’s happening towards reef health and ensuring that this ecosystem and the great barrier reef stays great,” she said.
Queensland Environment Minister Dr Steven Miles said that Raine Island is one of the most special places in the state.
“[Raine Island is] the most important turtle hatchery in the world, and it’s the site of a very special conservation project,” he said.