Michael Kennedy says Transport Minister Jacinta Allan's comments on ABC Radio on Thursday are wrong.

Ms Allan announced that work would begin on a 3.8-kilometre stretch of the highway at Dobie after an interim settlement was reached between the Traditional Owners and Major Road Projects Victoria.

Ms Allan told ABC Radio on Thursday that there had been plenty of consultation, as well as mediation around the project. She said her department had followed every regulation and requirement "every step of the way" as part of an independent planning process that was concluded in 2013.

Major Road Projects Victoria agreed that it will start works on a 3.8km stretch of the duplication, but not commence substantive works on the rest of the alignment until a decision is made on the appeal.

In return the applicants have agreed to make reasonable efforts to direct and encourage protesters on the site not to interfere with these works.

In a separate statement, Ms Allan said she was pleased works could get underway on a section of the project.

She said the upgrades were urgently needed and would commence within days.

"Even though the two registered groups that represent the Djab Wurrung people have formally approved the project, we have entered into this agreement as a show of good faith with the protesters," she said.

"We have entered into this agreement as a show of good faith with the project opponents but it is now time to let MRPV get on with this work as agreed."

Mr Kennedy disputed some of what Ms Allan said on radio on Thursday.

"I was disturbed at what I believe were some of her comments about 'some people' opposing the proposed duplication, that 'an independent planning process had been followed' and that 'the government had consulted very carefully with Indigenous groups' who gave approval to go ahead to avoid two trees," he said.

"There has been no consultation whatsoever with my clients, but rather with an Eastern Maar Aboriginal Corporation and a former Registered Aboriginal Party, Martang."

Martang and Eastern Maar are both bodies that were formed to represent Traditional Owners.

"Martang has been deregistered. A recent statement by Rodney Carver is rejected by my clients," Mr Kennedy said.

"The 2012 Environmental Effects Statement was not part of an independent planning process. It was prepared for VicRoads by its preferred consultants.

"It had systemic faults, as VicRoads found when it commissioned a peer review by a firm called Biosis in December 2015, as well as was established in two ecological reports commissioned by the local farmers in 2016. The EES failed to identify a nationally listed endangered grassland community.

"VicRoads has ignored these reports. The EES overlooked over 1600 large old trees."

Major Roads' previous estimates suggested about 1350 large old trees would be destroyed - a figure it originally estimated as 221.

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