The court ruled federal environment minister Melissa Price's December decision not to make declarations under the Aboriginal and Torres Strait Islander Heritage Protection Act to protect trees near the Western Highway to be "an error of law".

Jidah Clark and other Djab Wurrung people applied for the court to overturn the decision and grant protection in June last year, with the court taking a stance on Friday.

"In particular, it is conceded that the Respondent (Ms Price) did not afford the Applicants procedural fairness in making the Decision insofar as the Respondent took into account credible, relevant and significant information without putting that information to the Applicants and inviting them to comment on that information," Justice Debra Mortimer wrote in her order.

RELATED: Duplication plans altered

The court also ordered the environment minister to pay the legal costs of the applicants.

Activists set up camp at multiple sites along the highway near Buangor, ensuring any proposed works did not commence.

Elder Aunty Sandra Onus was also an applicant on the order. She said the federal court's decision adds to the string of wins activists have had in recent months.

"We are hoping everything will calm down and work will only be done in the areas we have asked for," she said.

"It is a lot better than all the damage they wanted to do.

"This order from the court means we can try and work through the alternative route we have provided that will significantly lessen the impact the duplication will have on our cultural heritage."

Ripon MP Louise Staley said the court's decision should not mean the project comes to a stop.

"The Federal Court decision is very clear that this decision is not a stop work order," she said.

"It specifically notes that the applicants would need to apply, with 24 hours' notice, to the Federal and State Governments for any urgent relief related to the Major Road Projects Victoria which affects the Western Highway Duplication.

"Plain and simple, work cannot just stop on this project."

A fresh decision will need to be made by the environment minister.

A stop-work amnesty was agreed upon between Djab Wurrung people's lawyers and Major Road Projects Victoria in late March, with an agreement made by both parties no work would commence until after 5pm on Monday, April 22.

Aunty Sandra said she believes work will be delayed until at least May now.

"This order will impact how they go about it now I think," she said.

"Despite that, people will stay to make sure nothing will be done to the areas in question.

"We believe what was going to happen was unreasonable and we will stick by that."

Major Roads Projects Victoria has been approached for comment.

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