The West Australian Premier has hardened his stance on the Roe Highway extension, warning protesters they will be arrested and charged if they attempt to physically block land clearing on the site.

There were 31 arrests resulting in 39 charges when police clashed with more than 1,000 protesters who invaded bushland today to halt site works on the controversial project, which is the first stage of a road for heavy haulage linking the city's industrial east to Fremantle Port.

Mr Barnett said opponents of the project had exhausted all legal challenges to the project and should let it proceed.

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He said he respected their right to protest, but that the scenes at Roe had gone beyond peaceful protest.

"That is interfering with people lawfully going about their work," he said.

He also slammed the people who clambered over a fence enclosing the construction site earlier today.

"This scenario, the fence 'fell over' give us a break," he said.

"The fence was pushed over. We're not going to put up with that sort of nonsense.

"People, if they continue to interfere with the work, they will be arrested, they will be charged, they will be fined."

Main Roads issued a warning to would-be trespassers, saying they would be putting themselves at risk with heavy machinery operating at the site.

The agency has now established an "exclusion zone" around the works, that would be broadened as the works continued.

Mr Barnett also defended his decision to push ahead with land clearing just eight weeks before the election, with the Opposition promising to scrap the project.

Charges laid after people lock on to trees, machinery

Police said a total of 39 charges were laid today, mostly for trespassing and obstructing public officers.

The protesters began arriving from first light, many carrying placards, while more than 100 police were also present, with reinforcements called in as the protest got rowdy.

Protester and Fremantle councillor Rachel Pemberton said about half of the thousand-strong crowd had walked inside the fenced area to support the three people chained to machinery and trees.

"This morning has been really extraordinary," she said.

Parts of a temporary fence were knocked down as police and protesters clashed. ( ABC News: Claire Moodie )

"We want to do all we can to minimise the destruction of this woodland."

She said the State Government should delay work on the project until after the election.

"This is a very, very expensive and unnecessary project and it should at least be put to the people," Ms Pemberton said.

A woman is one of two people who have chained themselves to machinery at the site. ( ABC News: Claire Moodie )

Other politicians at the protest include Labor's Chris Tallentire, Josh Wilson and Simone McGurk, and Lynn MacLaren from the Greens.

The Roe 8 project would extend the highway five kilometres as a dual carriageway road, from its current Kwinana Freeway end in Jandakot to Stock Road in Coolbellup, through the Beeliar Wetlands.

The Government says building Roe 8 will take 2,000 trucks off Leach Highway between the freeway and Stirling Highway each day, and thousands more off other surrounding roads.

WA Labor Leader Mark McGowan has defended the actions of protesters at the site.

"This road is a $2 billion waste of money," he said.

"A waste of money by the Government and if people want to protest about the Government wasting money that is the democratic right of people in Western Australia."

Labor has vowed to scrap the project if it wins the March 11 state election.