The booming humpback whale population has given researchers a chance to piece together a few remaining mysteries of the once-threatened species as large pods migrate north and south along the WA coast this year.

Murdoch University's Fredrik Christiansen and Kate Sprogis deployed drones to photograph and measure the body condition of female humpbacks on two legs of the year-long migration, which begins in Antarctica over summer.

In June, the pair spent three weeks assessing well-fed humpbacks as they moved north from the feeding grounds of Antarctica past Augusta, in WA's south west only to reunite with the emaciated females this month off Dunsborough on their return voyage.

Dr Kate Sprogis deploys a drone off the coast of Dunsborough. ( ABC South West: Anthony Pancia )

Female humpbacks will typically leave southern waters weighing their heaviest, on average between 30-40 tonnes, but will return substantially lighter having shed a lot of their weight feeding calves birthed in the warm northern waters off Australia's coast.

Exactly how much the females lose and the amount of energy they expend in the process remains a slight mystery and it's that key detail Dr Christiansen is hoping to deduce.

At both interactions with the migrating whales, the drone offered the chance to record measurements of the health status of the population, which Dr Christiansen said had not been recorded since the days of commercial whaling, which came to a halt in Australia in 1978.

Dr Christiansen monitors the drone as it hovers above humpback whales in Dunsborough, a coastal town in WA's south west. ( ABC South West: Anthony Pancia )

"There's no baseline information on the body condition or health of humpback whales," Dr Christiansen told the ABC just prior to heading out for a morning expedition.

"A lot of what we know comes from historical whaling records, so is fairly old and to some degree an approximation.

"The drone footage does allow us to study the different body shapes in much more detail.

"We know they come up from Augusta as fat as they will be and where we see them here along the coast of Dunsborough they will not have eaten for three to four months, so they will be at their thinnest."

A female humpback off the coast of Augusta in WA's far south west at the commencement of the annual migration. ( Supplied: Sprogis/Christiansen, Murdoch University )

The researchers secured permits to fly drones above the whales and Dr Christiansen said the use of drones would lead to findings at an exponential rate with the added benefit of being non-invasive to whales when they were often in a vulnerable state.

"The use of drones is really just starting to revolutionise the field of research, particularly in terms of understanding the physiology of whales," Dr Christiansen said.

"Body size, fat content and health is quite a basic metric to look at and for most terrestrial animals it is already really well known, but not for whales as it's so difficult to measure them with a single measuring tape or even being able to measure them in the first place.

"Consequently there is very little information about their size and condition.

"They are very protective of their calves so a drone puts us as close as we need to be without interfering with that relationship."

An emaciated female humpback on the southern leg of the migration in Dunsborough. ( Supplied: Sprogis/Christiansen, Murdoch University )

Initial signs also indicated there were around 30,000 humpback whales off the WA coast alone — a far cry from the fate they faced just less than 40 years ago.

"This population is recovering really well," Dr Christiansen said.

"It's also one of the healthiest populations of humpbacks on the planet, which is why we are working with them.

"Here we see them in natural conditions and a pristine environment so then we can compare them to other humpback populations, such as in the one in the Arabian Sea, which is not doing so well, so we can get a more global understanding of this species."

Dr Christiansen also cited populations off South America and Africa as examples of humpback whales recovering after heavy losses to commercial and illegal whaling, which led to numbers reaching as few as several hundred.

"It's really a success story," Dr Christiansen said of the continued growth of humpback whale populations.

"They really did face extinction because of whaling and I think the only reason it [whaling] stopped was because the whalers couldn't find any more whales."