Justice John Griffiths ruled that the appeal - originally made by Aunty Sandra Onus and Marjorie Thorpe - should be reconsidered by a minister other than Ms Ley.

The judgement noted that maps created for the project were inaccurate, and more importantly, Ms Ley had not viewed a map showing how close the highway would come to the trees.

"Notably, the map does not show the highway alignment at all, although it may be assumed that the alignment is somewhere in the Specified Area," Justice Griffiths wrote in their judgement.

"The scale of the map is such that the map fails to identify with any precision the physical proximity of each of the six trees to the assumed highway alignment. ...the Minister did not have before her any map which precisely identified the proposed highway alignment as at the date of her decision."

Justice Griffiths also ruled that the Federal Government was cover the applicants' costs.

The 12.5km section of the highway duplication project is already on hold due to separate action in the Victorian Supreme Court. An injunction on this case is in place until February 2021.