Plans to upgrade the Western Highway near Ararat have been met with protest after it was revealed it would see the destruction of several trees considered sacred by Indigenous people.

In a report tabled to parliament on Thursday, Victorian Ombudsman Deborah Glass said a modified route agreed last year between the Eastern Maar Aboriginal Corporation and Major Road Projects Victoria will retain 16 out of 22 trees identified as culturally significant, including two large birthing trees.

Read more: Two suspected overdoses in two months, amid allegations of drug use at secure sex offender facility

Ms Glass said it was not her role to determine the best route for the highway duplication, but she was satisfied government agencies made appropriate efforts to minimise the damage to Aboriginal cultural heritage.

"In light of these and other commitments, Eastern Maar has now indicated it is satisfied that Aboriginal cultural heritage impacted by the project will be adequately protected," Ms Glass said in a statement.

Ms Glass said her investigation was prompted by complaints from people opposed to the project, who said the government did not consult traditional custodians and ignored options that would have provided better cultural and environmental outcomes.

She said it was not surprising some Djab Wurrung traditional custodians continue to distrust public authorities associated with the project.

"That distrust - and the resilience displayed by some Djab Wurrung traditional custodians in seeking to protect their traditional lands - is hardly surprising considering past and ongoing Aboriginal experiences of government," Ms Glass said.

"I acknowledge it is not only the trees, but all the surrounding landscape that carries the weight of Aboriginal history."

The Western Highway project began in 2013 and is expected to be completed by 2021.

READ MORE:

AAP