The state government is planning to build an elevated station at the airport, but its operators favour an underground station at the facility.
A new train station will also be constructed at Keilor East and a sky rail bridge built over the M80 Freeway as part of the project.
In a statement, a Melbourne Airport representative said airport officials were yet to come to an agreement with the state government on the location or design of the airport connection.
"Melbourne Airport's preference has been, and remains, an underground station," airport ground transport chief Jai McDermott said.
"(It) provides a superior passenger experience, safeguards for future connectivity and is appropriate for Victoria's international gateway.
"It is important that the new rail station works for all airport users, not just those who arrive by train."
The business case, released on Wednesday, found the project will cost between $8 billion and $13 billion and would have a benefit-cost ratio of up to $2.10 for every $1 spent.
It said building an elevated station at the site would be quicker and less expensive to build, while there would be less of an impact on passengers during construction.
The Victorian and Australian governments are each contributing $5 billion towards the project.
Minister for Transport Infrastructure Jacinta Allan said the project, which is expected to be completed in 2029, would connect hundreds of thousands of people to Melbourne's train network for the first time.
The project is expected to create opportunities for local workers and businesses.
The state government says trains between the city and airport would run every 10 minutes and the journey would take about 30 minutes when the project is finished in 2029.
It would also include 12 kilometres of extra track and an upgrade to Sunshine Station.
In response to Melbourne Airport's push for an underground station instead of above ground, Premier Daniel Andrews said he sought advice from expert engineers.
"I know the airport's got a different view, I don't necessarily know that they're paying for the project so they may have all sorts of views," he said.
Ms Allan said the fare structure would be finalised closer to 2029.
"We've used some assumptions in the business case that are comparable to the costs that are used at say Sydney Airport at the moment, where there's a standard fare plus $1 or $2 extra as a bit of a premium," she said.
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