Melbourne Airport is conceding on its push for an underground station and will back the state and federal governments' preference for an above ground one.
The Victorian government argued the surface option would be quicker and cheaper and the airport thought an underground facility would future-proof it.
"Victorians have waited long enough for an airport rail line," Melbourne Airport chief executive officer Lorie Argus said on Monday.
"We will work with the Victorian government to deliver their preferred above-ground station at the airport so the rail line can become reality."
Melbourne Airport's Lorie Argus says a compromise has been reached so work can finally begin. (Diego Fedele/AAP PHOTOS)
The airport's plans for a third runway are currently being considered by the federal government and if and when it opens, 45 million travellers a year are expected to pass through.
"We are prepared to compromise on our position to ensure we have more transport options in place for the millions of new passengers that will visit Victoria and the airport precinct's expanding workforce," Ms Argus said.
The airport hopes talks on the project's design, construction and land acquisitions could restart immediately.
The compromise comes two weeks after federal government-appointed mediator Neil Scales declared the underground station should no longer be entertained.
Mr Scales found the $10 billion link remained "viable and necessary" but should be above ground unless a comprehensive case was put forward for an alternative.
The Victorian government repeatedly said an underground station would cost too much.
The airport welcomes some 100,000 passengers a day and is the largest employment hub outside Melbourne CBD.
President of the Public Transport Users Association Tony Morton said an above ground station would still be a game-changer for millions of passengers.
"This is a way to get the project going and provide value for the Victorian public," he told AAP.
"After that we can focus on some of the other important factors like access between the station and terminals and transport within the airport."
In 2018, the Victorian and federal governments each committed $5 billion to the project, which is expected to cost between $8 billion and $13 billion.
Melbourne Airport was part of a consortium the following year that offered up to $7 billion towards an underground station and express tracks from Sunshine to Southern Cross.
The stand-off between the parties meant the state government in May delayed the project, pushing its completion back four years to 2033.
Melbourne Airport's land is leased by the Commonwealth to the Australia Pacific Airports Corporation Limited under a 50-year deal, meaning any planning application must be submitted by the airport.
