The Commonwealth has appointed Mr Scales to resolve a long-running stand-off between the Victorian government and Melbourne Airport's operators over whether the airport railway station should be elevated or underground.
Mr Scales, a High-Speed Rail Authority board member and former director-general of Merseytravel in the UK, has begun the work and plans to visit the airport later this week.
In November, federal Infrastructure Minister Catherine King flagged she would appoint an independent mediator to resolve the dispute after the mega project was spared the axe following a federal infrastructure review.
Melbourne Airport prefers the project's airport station to be built underground but the Victorian government is pushing for it to be elevated, arguing it would cost taxpayers $1 billion less, take two fewer years to build and cause less disruption.
A Victorian government spokesman welcomed Mr Scales' appointment to resolve the airport's "unreasonable demands".
"These frustrating negotiations have caused significant delays to the project," he said.
"We look forward to the Commonwealth progressing matters with Melbourne Airport so that we can continue to deliver the major projects that Victorians need."
The Victorian and federal governments have previously committed to contributing $5 billion each to the project, which is expected to cost between $8 billion and $13 billion.
The rail line to connect Melbourne to Tullamarine was originally due to be completed by 2029, with new and redeveloped stations in Melbourne's west.
Melbourne Airport's land is leased by the Commonwealth to Australia Pacific Airports Corporation Limited under a 50-year deal.
A planning application for the Commonwealth-owned land can only be submitted by the airport.
The airport and Ms King's office have been contacted for comment.
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