Drilling for the controversial Roe 8 highway extension has begun at Beeliar wetlands in Perth's south, where placard-carrying protesters have confronted workers.

About 60 protesters staged a sit-in at the Bibra Lake site, blocking the path of drilling and support vehicles from Main Roads.

However, police were eventually able to escort the vehicles and machinery from the area to another drilling site nearby.

More than two dozen police, including two on horseback, were at the scene, and there were verbal confrontations between protesters and Main Roads staff.

The vehicles entered bushland this morning to install monitoring bores as part of preliminary site work for the proposed Roe 8 highway extension.

A number of residents and environmentalists had occupied the track to the site, and were warned by police they faced arrest if they did not move.

"I'll give you some leeway, but at the end of the day you're blocking the access route here, which is blocking the contractors in," Inspector Darren Wynne told the crowd.

"You must allow them to move freely and go about their lawful right.

"We don't want to have to get to a situation where we have to enforce those rulings."

The protest ended peacefully at 2:00pm when Main Roads workers packed up the drilling rig and left the area.

Project 'shambolic': Cockburn mayor

Opponents of the highway extension tried to stop the drilling work by blocking the path of a Main Roads vehicle. ( ABC News: Jade Macmillan )

Earlier, Cockburn Mayor Logan Howlett urged the workers to stop drilling.

"We need to say stop, desist from any further activity until we've had a conversation with the managing director of Main Roads, and also the court case that is due to be heard next week," he said.

"[Desist until] the outcomes of that are known."

Main Roads used a drill rig to install monitoring bores at Bibra Lake as part of preliminary site works. ( ABC News: Jessica Strutt )

Mr Howlett said the project had been undertaken in a "shambolic" fashion without community consultation.

The Government wants to extend the Roe Highway across the wetlands and the project was planned as the first stage of the Government's Perth Freight Link, a $1.6 billion heavy transport route connecting the industrial area of Kewdale with the port.

Under the plan, Roe Highway would be extended from Kwinana Freeway to Stock Road, with stages two and three connecting it to Fremantle, and then across the Swan River to the port itself.

But earlier this month, Premier Colin Barnett shelved the final stages of the project, citing cost and complexity, and reinforced the Government focus on existing key projects like Roe 8, the Forrestfield Airport Rail Link and the Swan Valley bypass.

More than 1,000 opponents of the $500 million project rallied at the wetlands on the weekend, pledging to halt the project.

Mr Barnett today warned protesters at Beeliar not to disrupt work on the highway extension.

Loading

"If people are going to protest, that is their right, but I hope that they do it in a peaceful way and don't disrupt the work or put people's lives in danger," Mr Barnett said.

"We will not tolerate any violent or aggressive protests. Passive ones, fine."

Rethink the Link spokesperson Kim Dravnieks said about 40 protesters rushed to the wetlands after hearing there was a large police presence and a Main Roads drilling rig at the site.

"We are asking why they are doing these works only a week before the Supreme Court will be hearing whether these works are actually illegal," she said.

"We believe these works are probably trying to intimidate us. This road should not be built until all solutions are looked at."

Save Beeliar Wetlands convener Kate Kelly accused Main Roads of inflaming the situation and said it could have been avoided.

"It's absolutely over the top. No wonder people are cross," she said.

Protesters converge on Parliament

Speaking to a group of protesters at Parliament House, Opposition Leader Mark McGowan described the police presence at Bibra Lake as a waste of resources.

"This road needs to be stopped," he said.

"It is a huge waste of money, it is a road to nowhere, it doesn't fix any problems and the Government is going to be placing scores and scores of police officers on a daily basis, because the public are saying they don't want this road built."

More than 100 people gathered on the steps of Parliament to voice their opposition to the project.

Mr Barnett and Transport Minister Dean Nalder also addressed the crowd.

Mr Barnett insisted the Roe 8 extension would go ahead, and said the work in Bibra Lake was required to check environmental conditions at the site.