Perth Airport's expansion plans have cleared a major hurdle, putting a decades-old proposal for a third runway a step closer to reality.

But Aboriginal Affairs Minister Ben Wyatt's decision to grant Aboriginal heritage approval for the runway sparked an immediate backlash, with Noongar groups angry about the impact on a nearby sacred site.

The new airstrip, which is unlikely to be operational for about a decade and still has some hurdles to clear before it can proceed, will be constructed in part on Munday Swamp and will run parallel to the existing main runway.

Munday Swamp is an ancient turtle-fishing site deemed to be of high cultural importance to the Noongar community.

Aboriginal Affairs Minister Ben Wyatt says passenger demand warrants a third runway. ( ABC News: James Carmody )

Mr Wyatt pointed to the need for a third airport runway, pointing to passenger demand, but conceded his decision would anger some in the Noongar community.

"I appreciate the hurt my decision today may cause a number of Noongar people," Mr Wyatt said.

"I take no pleasure in this announcement.

"However my ministerial responsibility to protect Aboriginal cultural heritage must take into account the broader interests of the whole state of Western Australia."

The decision sparked an immediate backlash from some campaigners, with the South West Aboriginal Land and Sea Council "deeply disappointed" with Mr Wyatt's decision.

"The proposed new runway would destroy the cultural, historical and spiritual significance of the Munday Swamp, which is already acknowledged as being sacred to the Whadjuk Noongar People," the council said.

Rottnest Island Deaths Group Aboriginal Corporation director, Iva Hayward-Jackson. ( ABC News: Jacob Kagi )

Iva Hayward-Jackson, a director of the Rottnest Island Deaths Group Aboriginal Corporation, said he was angry and disappointed with the decision.

"It is damaging to our spirit, to our culture, to our sacred land and our sacred waterways," he said.

"This is a sacred area that is ancient ... there are 30,000-plus years of Aboriginal heritage and culture at that particular site."

Perth Airport said the parallel runway, to be built to the south-east of existing airport infrastructure, was needed to cater for an expected surge in demand.

The location of a proposed new third runway for Perth Airport. ( Supplied: Perth Airport )

The airport is predicting it will see 35 million passenger movements by 2045, up from 13.6 million currently.

"Two distinct flight paths are much safer, it allows for much more frequency of flights taking off and landing," Perth Airport chief executive Kevin Brown said.

"In our region there is a lot of opportunity and we want to make sure we are providing that full opportunity."

Mr Brown said everything possible had been done to minimise the impact on Munday Swamp, including shifting the proposed runway further away from that site than initial plans had proposed.

"Ninety per cent of the swamp will be protected for future generations," he said.

The airport's expansion plans will see Qantas shift its operations to the 'Airport Central' precinct, near the international terminal, by 2025.