A national body which advises UNESCO on world heritage sites will raise its concerns with the WA Government about the deregistration of Aboriginal sites along the route of the controversial Roe 8 project.

The WA representative of Australia ICOMOS (International Council on Monuments and Sites), Tom Perrigo, said the board had asked him to discuss its concerns over the removal of protection of important Aboriginal sites, including some around Bibra Lake, with Aboriginal Affairs Minister Peter Collier.

"It appears [the deregistration] is in association with the development of Roe 8 and that's of great concern," he said.

Mr Perrigo, who was for 25 years the head of the National Trust of Australia (WA), said he was concerned about a lack of transparency about the reasons behind the deregistration of Aboriginal heritage sites.

"The deregistration of sites is something that has not been clearly articulated," he said.

"Aboriginal people as well as non-Aboriginal people don't understand why these sites are being deregistered and the Government has lacked transparency and has shown little accountability.

"Those two are the twin pillars of good governance."

Mr Perrigo said Aboriginal heritage should be a key focus of Heritage Minister Albert Jacob's portfolio.

Some culturally significant Aboriginal sites around WA have been deregistered in the past year on the basis they no longer fit the definition of a sacred site.

These include two sites around North Lake and Bibra Lake which could be significantly affected by the planned extension of Roe Highway from its Kwinana terminus to Stock Rd, as part of the $1.6 billion Perth Freight Link project.

They were removed from the register last year as a result of a recommendation by the Aboriginal Cultural Material Committee (ACMC), which is part of the Department of Aboriginal Affairs.

The areas around the lakes are considered by Indigenous people to be sacred because of the legend of a giant serpent called Waugul.

Another site covering Bibra Lake has not been deregistered but its heritage value was a key reason behind the committee's 2013 decision to refuse approval for the Roe 8 project, although the decision was reversed last year.

Transparency concerns over Aboriginal heritage site management

Tod Jones, a senior lecturer in planning and geography at Curtin University, is also concerned about the lack of transparency in the management of Aboriginal heritage sites.

"What's meant to be a system for the management of Aboriginal heritage ends up being a way that Aboriginal heritage can't affect the development of projects," he said.

But the Department of Aboriginal Affairs rejected claims of a lack of transparency and said sites around Bibra Lake were deregistered before decisions around the construction of the Roe Highway extension were made.

"All information provided was considered by the ACMC, in addition to the fieldwork undertaken as part of the assessment," it said in a statement.

"The decision made by the ACMC does not put any significant heritage sites at risk."

The department said the register of Aboriginal heritage sites was public and that ministerial decisions were published on the department's website.