Western Australian wildlife carers fear they may have to euthanise joeys because the cost of flying the native animals is twice as much as cats and dogs.

Broome-based wildlife carer Jan Martin struggles with the cost of flying marsupials.

She also sometimes needs to fly kangaroos 1,000km from Broome to Kununurra, a route only serviced by regional carrier, Air North.

The animals need to be transported to be raised by other wildlife carers or to be released back into the wild.

"I usually send them in pairs, so to send two little joeys, each five kilos, it's going to cost me $663. A dog would cost me $155," Ms Martin said.

Jan Martin with an orphaned joey at her wildlife rescue centre in Broome. ( ABC News: Natalie Jones )

Rose Best, from the Pilbara Wildlife Carers Association, rehabilitates about 120 kangaroos every year.

Due to a lack of local carers, some animals are sent from her home in Karratha to Perth, using Qantas or Virgin, which uses third party providers to manage its cargo unit.

"Our biggest problem is we can send them down, but the reds [kangaroos] come back up for release," Ms Best said.

"We're being charged $1,200 to send three red kangaroos back.

"It is totally cost prohibitive. We don't get much funding or support anymore, so when you're looking at nearly a third of your income going out in freight, we just have to say we can't do it.

"Unfortunately, there are eagles and birds of prey who need food.

"We might just have to put the joeys down and use them as meat."

Kangaroo branding 'not justified'

A disgruntled wildlife carer says Qantas should change its emblem. ( ABC News: Giulio Saggin )

Ms Martin believes Qantas should remove its famous animal branding known as the Flying Kangaroo.

"Take the big red kangaroo off the tail because they don't offer a service to wildlife," she said.

"Qantas is the Australian airline, you've got a kangaroo as your emblem, you use Australian wildlife with all your advertising and your touristy stuff and yet when one needs help…

"You want to charge me more than you charge that 10kg dog there."

Wildlife needs extra care, Qantas says

Qantas defended the cost of transporting the kangaroos, saying the price discrepancy between pets and wildlife was due to the extra care needed to transport native animals.

"Kangaroos have never been classified as pets and animals, [because] kangaroos require more care than a domesticated animal such as a dog or cat, which is partly why there is a cost difference," a Qantas spokesperson said.

Pilbara Wildlife Carers responds to more than 5,000 emergency calls each year. ( Supplied: Pilbara Wildlife Carers Association )

But the wildlife carers said kangaroos did not receive different treatment from pets on flights.

"They don't have different temperature requirements or anything like that," Ms Best said.

"The only consideration that we ask, that I think any cat or dog owner would ask, is that the crate isn't left sitting on the hot tarmac."

A Qantas spokesperson has told the ABC they are happy to work with wildlife carers on different options.

Editor's note (8/12/2017): The original version of this story stated that Air North is a subsidiary of Qantas, which was not correct. It has since been updated, along with a response from Qantas.