West Australian Premier Colin Barnett's decision to shelve stage two of the Perth Freight Link to Fremantle has raised doubts about the State Government's plans to recoup part of the $1.6 billion project's cost with a toll on trucks.

The truck toll, referred to by the Government as a heavy vehicle user charge, would be the first of its kind in WA.

The Nationals, who are in an alliance with the Liberals, have already raised concerns about how it would work and what other roads could be hit with the toll into the future.

The Government has committed to building the Roe 8 highway extension from Kwinana to Stock Road and was due to award contracts for Roe 9, linking the road to Fremantle by the end of the year.

But earlier today Transport Minister Dean Nalder said he did not know when the second stage of the project, which involves demolishing homes in Palmyra, would go ahead.

In December, the Federal and WA Government said in a joint statement that the per kilometre charge would apply to heavy vehicles between Muchea and Fremantle, and would start once the road was finished.

Mr Nalder confirmed that was what the Government had been working towards.

"It's something that we'll need to revisit and something I'll need to have further discussion with the Premier on," he said.

Asked if there could be a scenario where the truck toll would only apply to a smaller section of the Perth Freight Link, Mr Nalder indicated that was not the preference.

"We want the flexibility to continue to work with the industry because if we get this model right, it may allow us to bring forward additional projects that mean we do actually expand it further but only if there's an economic benefit to industry," he said.

Nationals concerned about toll

The Government was recently poised to introduce legislation, approved by Cabinet, to Parliament that would have enabled the truck toll, but it was pulled at the last minute after the Nationals raised concerns.

WA Nationals leader Terry Redman confirmed he was working with Mr Nalder to clarify aspects of the bill.

"I think the pitch that's being pushed is that the tolls that will be put on the infrastructure will be more than covered by the savings of anyone using it," he said.

"I think there are other elements to the bill in respect to tolls and how you might put other roads on that that were concerning.

"There's obviously landing points that are being worked through but the Nationals have got that and a couple of other issues that they are working through with the Minister.

"That's the point that's being clarified, in respect to what other roads might be put into the category of saying we're going to charge a toll and this and just what the process is in and around that."

Opposition transport spokeswoman Rita Saffioti said Labor would closely scrutinise the legislation when it was introduced to ensure it was not providing an open slather for truck tolls.

"The ability to put tolls on other roads, not only the prescribed roads... not only the new roads, is of great concern," he said.

"We know that Dean Nalder and Colin Barnett can't agree on anything and of course now the National party is trying to distance itself from this project and this potential toll."

She said the number of issues the Nationals and Liberals were at odds on continued to grow.

The ABC has also been told that some Nationals are also concerned the legislation will further expand the powers of the WA Commissioner for Main Roads, Reece Waldock, but Mr Nalder was confident a deal could be struck.

"We believe it's done in a responsible way but we're going to work it through with the National Party to make sure all the parties are comfortable," Mr Nalder said.

He expected the legislation to be introduced this year.