The Federal Government has rejected an Indigenous group's eleventh-hour attempt to protect culturally significant trees that would be cut down as part of a major highway duplication in western Victoria.

In June last year, a group calling itself the Djab Wurring Heritage Protection Embassy submitted an application seeking protection for an area at Buangor under the Aboriginal and Torres Strait Islander Heritage Protection Act.

The appeal brought the State Government-run project to a halt until a decision was made. The project was supposed to begin in June last year.

In the weeks leading up to the submission, protesters had set up camp to physically protect trees they said had invaluable Aboriginal cultural heritage.

The trees are among 3,000 due to be removed to make way for the project.

The $672 million project to duplicate a section of road between Ararat and Buangor has faced a string of complications and delays over the years, including a planning administrative error that delayed it by a full year in February 2017 and Supreme Court action by sheep farmer MairiAnne MacKenzie.

Decision made on basis of community safety

A statement from the Federal Department of the Environment and Energy said Environment Minister Melissa Price's decision not to protect the area or objects was made based on a report commissioned by former Environment Minister Josh Frydenberg.

In addition, she had relied on advice from former Victorian Roads minister Luke Donnellan.

The project is being managed by Major Road Projects Victoria.

An artist's impression of what the Western Highway duplication will look like between Buangor and Ararat. ( Supplied: VicRoads )

"The decision not to make a declaration was on the basis of the significant road safety upgrades that the Western Highway upgrades would provide to the wider community (being the current route had a road toll of 11 fatalities and 49 serious injuries on that part of the highway in the period 2010-2015)," the statement said.

"In further support of this decision, Major Road Projects (Victoria) committed to avoiding one tree and to undertake further consultations, which could result in the avoidance of other trees."

The statement said Mr Donnellan had written to Ms Price to tell her he was: "satisfied that there is effective protection of Aboriginal cultural heritage in the area".

Major Roads Project Victoria development and performance director Andrew Williams said the organisation was: "taking the time to fully consider the decision by the Federal Government and what it means for the delivery of this stage of this stage of the Western Highway Duplication".

'Decimation of cultural heritage' says elder

Djab Wurring Heritage Protection Embassy member and elder Aunty Sandra Onus said she was disappointed but not surprised by the outcome.

She had not been notified of the Federal Government's decision, which was made on December 19 last year.

Ms Onus said the trees at risk of being removed include significant birthing trees and an alternative route that goes around the trees should be considered.

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

"I'm not against progress — we need to be safe too — but I am against the decimation of our cultural heritage, especially when an alternative route is being offered," she said.

Ms Onus described one birthing tree as "absolutely beautiful".

"It's been there for a long time and one can imagine that many Aboriginal babies have come into the world there with their mothers," she said.

"The thought of them destroying something that has such a long association with Aboriginal people and a practice that goes back 60,000 years, it just blows my mind.

"That area is a wealth of Aboriginal artefacts and heritage.

"It's just sad that these people can't just have a listen to us and have a bit of empathy and understanding."

Ms Onus said although she was disappointed with the decision, she was hopeful about the department's statement mentioning the avoidance of particular trees.

She has vowed to keep physically protecting the trees and to consider other legal action.

"The plan is to go as far as we can; that's all one can do," she said.

Dispute over cultural assessment

The Victorian Government has previously said that a cultural heritage management plan for the project had been approved by traditional owners, including Martang Incorporated and the Eastern Maar Aboriginal Corporation.

A statement released by the Department of Premier and Cabinet in June last year said both groups: "have stated they do not believe the trees to be birthing trees or to otherwise have cultural significance".

But Eastern Maar Aboriginal Corporation CEO Jamie Lowe said his organisation was not involved in the cultural heritage management plan.

He said his organisation had been undertaking its own assessment of the area, including the trees, and it was working with Major Roads Authority Victoria.

"We'll fight pretty hard for them to be preserved," Mr Lowe said.

He said there was a broader issue with the way Aboriginal cultural heritage was treated.

"Fundamentally, it comes down to a system where our set of values of cultural heritage don't necessarily line up to the system's value of cultural heritage," he said.

"That's where these situations arise.

"If we send an application to the state government or the federal government, even though they have their thresholds of what is cultural heritage, our measures are different as a community.

"A lot of our cultural heritage exists in the form of rock art, artefacts and in this case, the trees.

"It's something that we value. We know our ancestors have walked that land and created scars on trees or used them as birthing trees.

"We know that our ancestors have been there and it's something that we hold in high regard."

Martang Registered Aboriginal Party is the registered traditional owner group for the area, and through its involvement in assessing cultural heritage as part of the duplication, it did not identify the trees as having cultural significance.

Editor's note 31/01/2019: This story has been updated since its original publication date of 25/01/2019 to clarify the road toll statistics on the highway.