West Australian Premier Colin Barnett has confirmed plans to shelve stage two of the controversial Perth Freight Link project, saying the State Government "might see where we're at in 12 months' time".

Mr Barnett conceded the project, which has encountered fierce community opposition, was more "expensive" and "complex" than the Government had anticipated.

Until recently, Transport Minister Dean Nalder had insisted a final route and construction contracts for stage two would be finalised by the end of the year.

The second section of the project was intended to link Roe 8, the first section of the freight link, to Fremantle Port.

Mr Barnett said the Government was going to focus all of its efforts in 2016 on three major projects: Roe 8, the Forrestfield Airport Link and the Swan Valley bypass.

"We might see we're we're at in 12 months' time, but for the moment all of our effort is Roe 8, the rail line to the airport and Forresfield and the Swan Valley bypass. They are the highest priorities," he said.

"They are more important and they're happening first. They're the ones that we're ready to go on."

The decision effectively puts stage two on hold until after the state election in March 2017.

However Mr Barnett also appeared to question the merits of proceeding with stage two, based on the cost and difficulty of the plans.

"I'm not about to rush into a decision on a link from the end of Roe 8, yet to be built, to the Fremantle Port. Because it's incredibly complicated, incredibly expensive for what it does," he said.

"We've also got one eye firmly on the construction of an outer harbour at Cockburn so the decision will also be influenced by that."

Freight link now even less defensible: Labor

Federal Member for Perth Alannah MacTiernan said she wanted the Federal Government to withhold funding for the Perth Freight Link.

"Today's reports confirm what we've been saying for months - that Mr Barnett has no intention of building section two of this chaotic project," Ms McTiernan said.

"The already limited business case and cost-benefit analysis of the project is based on a two-stage road - the Roe 8 extension and a link to the Fremantle inner harbour.

"We do not support this project as it was originally conceived, but it is even less defensible to build half the project and destroy a valuable wetland in the process."

Ms McTiernan said it was time for the Turnbull Government to take some responsibility over the Perth Freight Link.

"The Federal Government cannot hand $925 million of taxpayer dollars to the Barnett Government if it only intends on building half the project," she said.

"Malcolm Turnbull must demand clarity from Mr Barnett on what his Government actually intends to build before signing off on any Federal funding for the Perth Freight Link."

Earlier this week, Mr Barnett was surrounded by protestors and heckled in Bibra Lake as the Government announced that Leighton Contractors would build stage one of the project.