A group that has fought a long-running campaign against the next stage of work to duplicate the main road connecting Melbourne and Adelaide fears time is running out to halt the "unnecessarily destructive and expensive" project.

VicRoads has sought fresh approval from Planning Minister Richard Wynne to proceed with the 5.5-kilometre section of road between Buangor and Ararat in western Victoria after the previous authorisation expired.

The Keep the Original Route (KOR) group said six trees of Aboriginal significance had recently been identified, including birthing, scar and canoe trees, which will be felled or put at risk by VicRoads' planned alignment.

VicRoads has previously admitted environmental studies supporting the project included "errors and inconsistencies" and a "significant underestimation of large old trees" to be destroyed.

KOR has proposed an alternative alignment, which would create a new carriageway next to the existing highway, rather than creating a new section of road through farming properties.

The centre tree is said to mark a place where Indigenous women gave birth. ( ABC News: James Hancock )

Calls for independent review

The group, which represents several affected landholders and more than 200 other concerned locals, has been arguing against the project in the Victorian Supreme Court and wants an independent panel to examine which option is better.

MairiAnne MacKenzie, who will have part of her property compulsorily acquired for the duplication, said the Indigenous trees were not identified by VicRoads during the planning process.

She said it added to a growing body of evidence suggesting the environmental assessment process was riddled with flaws and the proposed upgrade would be too harsh on the environment.

"It's rare, it's precious, we don't want to live in a world with no past," Ms MacKenzie said.

"We're not trying to stop the road, we're trying to reduce damage and save taxpayers money."

Ms MacKenzie said several independent engineers and environmental consultants had found their option would be cheaper and quicker to build, while having less impact on the environment.

"[Ours is] $65 million less than what has been announced," she said.

"Around 25 large old trees [destroyed] on the route we're proposing, it would be around 90 trees on the route VicRoads is currently planning."

Gunditjmara Djab Wurrung elder Ted Lovett said the six Aboriginal trees would be protected by following the KOR group's route.

"They're taking out heritage really," he said.

"Over 500 years old and they're very rare trees."

Mr Lovett said not all Indigenous people in the region had been properly consulted about the project because the State Government had only been dealing with the registered group, the Martang Aboriginal Party.

Aboriginal Victoria denies the six trees are of historical significance but Mr Lovett supports the call for an independent panel to examine all of the data and get to the bottom of the dispute.

"It should be Djab Wurrung, not just the one family making all the decisions," he said.

Indigenous elder Ted Lovett beside what is said to be a tree from which bark was cut centuries ago to build canoes. ( ABC News: James Hancock )

'Expensive intrusion across farmland'

An engineer and VicRoads adviser, David Clark, told the Supreme Court the route put forward by the KOR group would be quicker to build than the VicRoads proposal.

"Scheduling the construction of the works could be staged to be done in three stages, two of which could be done simultaneously," he said.

"I informed the meeting that in my opinion those works could be completed in 18 to 24 months."

Another engineer, James Higgs, told the court VicRoads' alignment would involve an expensive intrusion across farmland.

"[The KOR proposal] seemed to me to offer significant cost and time-to-construct advantages because it utilised much of the existing Western Highway pavement in the subject section of the project," he said.

VicRoads chief executive John Merritt declined to comment about the project while the matter was before the court.

"The Supreme Court action doesn't stop in progressing with the project," he said.

"Given that the matters are before the Supreme Court it's just not appropriate for us to litigate that matter outside of the court process."

If VicRoads gets the green light from the minister and the court, it is planning to start work by the end of winter.