The two had been locked in an impasse over whether a station should be underground or elevated as part of the Melbourne Airport rail project.
The government argued the above ground option would be quicker and cheaper and the airport thought an underground facility would future-proof it.
On Monday, Melbourne Airport Chief Executive Officer Lorie Argus said it was time to get on with the project.
"Victorians have waited long enough for an airport rail line," she said.
"We will work with the Victorian government to deliver their preferred above-ground station at the airport so the rail line can become reality."
Ms Argus said while the airport had consistently advocated for an underground station, she was prepared to compromise to ensure more options were in place for passengers and staff.
The airport would welcome an immediate recommencement of discussions over the station with an initial focus on its design, the sequencing of construction and redress for the land required for the above ground option, she said.
The compromise comes weeks after mediator Neil Scales declared the underground station should no longer be entertained.
Mr Scales found the $10 billion project remained "viable and necessary" but should be above ground unless a comprehensive case was put forward for an alternative.
The airport welcomes some 100,000 passengers a day and is the largest employment hub outside Melbourne CBD.
Plans for a third runway, currently before the federal government for approval, means passenger numbers could double.
In 2018, the Victorian and federal governments each committed to contributing $5 billion to the project, 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.
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