Unmanned aircraft used to protect soldiers in Afghanistan are now flying over south-east Queensland.

Scientists on Stradbroke Island are controlling the drones for a landmark study on humpback whales, launching them into Queensland skies.

The aircraft are made by Boeing subsidiary 'Insitu' and are normally used to protect soldiers in Afghanistan.

Now, they're surveying our waters, for pods of humpback whales.

Researcher Dr Amanda Hodgson, said the study was exciting but nerve-wracking.

"It's definitely very exciting but it's also very nerve-wracking because you never know what you're going to get, until you get out here," Dr Hodgson said.

Researchers are hoping the results will be accurate. It could mean a take over from traditional manned surveys.

Dale McDowall from Insitu Pacific said the survey was an opportunity to avoid the dangerous missions that had been undertaken in the past.

"It's an excellent opportunity to replace the dull, dangerous and dirty missions," Mr McDowall said.

The drones can be in the air for more than 20 hours and can fly at low altitudes, which would be risky for pilots.

Large parts of our coastline have never been surveyed for whales, but using unmanned aircraft would mean easier access to those remote areas for the first time.

The drone's flight path is monitored from headquarters and a camera in the front takes images and sends them in real time.

Chief Pilot, Dean Gilligan said the information was then sent back to the main control station for processing.

"And it's then transmitted to that big antenna where it comes down to our grand control station."

The study should provide a detailed record of whale numbers and their migration patterns.

If it's a success there may be a possibility the unmanned aircraft could be used for commercial use.

Mr McDowall said the drones were also able to be used to monitor gas and oil pipelines in support of energy companies.