The West Gate Tunnel Project and North East Link Authority will be moved under the control of Major Road Projects Victoria, Transport Infrastructure Minister Jacinta Allan confirmed on Thursday.
She said the merger was in part due to the Victorian government's budget measure to save $2.1 billion through cutting back spending on the public service, labour hire and consultancy firms.
Ms Allan described it as an administrative change and said it was premature to say how many jobs could go.
"It's reflective of how there is a responsibility on all of us to make sure that we are being efficient in the delivery of our services and how we work through these programs," she told reporters.
"But it is also reflective of where different projects are at their life cycle."
In a memo, Major Transport Infrastructure Authority director-general Kevin Devlin said the proposed new structure included roles for everyone with the three teams.
But he conceded there would likely be some duplication of roles, particularly within corporate disciplines.
Community and Public Sector Union Victorian secretary Karen Batt said the transport department had guaranteed there would be no job cuts from the merger during a briefing on Thursday morning.
"What they've said to us is they've got large numbers of duplication arising from this but we also have significant vacancies in the various areas arising from the COVID change," she said.
"So what they want do is have at least six to 12 months of working through how you job-match people to the vacancies that exist."
Ms Batt said she found the deputy premier's comments disingenuous and called for her to issue a clarification.
"The government does not need to go into wholesale redundancies to manage the downsizing of the numbers employed," she said.
"It can be done in a far more humane way ... people who are getting close to retirement should be given an opportunity to go with dignity and not have the ignominy of being told that they're redundant."
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