West Australian Premier Colin Barnett has thrown in the towel on stage two of the controversial Perth Freight Link project.

Mr Barnett has conceded that the project would have been more “expensive” and “complex” than the Government anticipated.

The plans also encountered fierce community opposition.

The second section of the Freight Link would have connected Roe 8 - the first section - to Fremantle Port.

Mr Barnett said the Government would now focus on other major projects: Roe 8, the Forrestfield Airport Link and the Swan Valley bypass.

“We might see where 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 Forrestfield and the Swan Valley bypass. They are the highest priorities,” he said on Sunday.

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

Stage two is now expected to stay on the shelf until after a state election in March 2017.

“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,” Mr Barnett 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.”

Federal Member for Perth, Labor’s Alannah MacTiernan, says ditching stage two make the whole project hard to defend.

“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 told reporters.

“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.

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

“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.”