Construction of the Perth freight link will begin in early 2016, with the project expected to remove up to 500 trucks a day from Leach Highway, the WA Government has announced.

Premier Colin Barnett said the state would put $650 million towards the almost $1.6 billion project, while the Federal Government has already committed $925 million.

Trucks will pay a toll to use the freight route between Muchea and Fremantle to recoup part of the cost of the project.

The link project will start with the Roe 8 project and extend Roe Highway through to Stock Road.

Mr Barnett acknowledged there was some controversy over extending Roe Highway because of environmental concerns.

Protest group Save Beeliar Wetlands is concerned the project will destroy one of the last wetland chains on the Swan coastal plain.

"It will either go through or over the Beeliar wetlands but those wetlands will be protected and indeed public access and usage of that environment will be very much enhanced," the Premier said.

"I'm absolutely confident the wetlands will not be permanently damaged... the protection of the wildlife in the area is assured.

The Save Beeliar Wetlands group is concerned about the impact of the extension on the Beeliar wetlands.

"The project's a good project... it very much improves the competitiveness of industry, it will help attract investment and it will be safer for people in the southern suburbs by getting heavy vehicles off other roads."

Asked if the Government would consider banning trucks from using alternative routes to avoid paying the toll, Mr Barnett said that was possible.

He said part of the project would include a major upgrade of the interchange near the new Fiona Stanley Hospital, an area that risked becoming a congestion problem.

Transport Minister Dean Nalder said the toll on trucks would only start to be charged once the entire link was up and running in 2019.

He said while about 38 hectares - about six hectares of that in the Beeliar wetlands - would be affected by the project, the Government proposed to purchase more than 400 hectares of native vegetation as an environmental offset.

But the Opposition's transport spokesman, Ken Travers, said the announcement marked the beginning of tolls for all vehicle users in WA.

"It doesn't matter how they dress it up, this is a toll road on our trucks and it will spread to cars," he said.

"Mr Barnett - before the election - promised no tolls full stop.

"Mr Barnett has cancelled all of the public transport projects ... when he cancelled those he said he didn't have the money and yet now they've found the money to dance to the tune of Canberra."

The Environmental Protection Authority approved the highway extension in 2013 after a review process that attracted more than 3,000 public submissions.