The state government is reportedly planning to build an elevated "sky rail" station at the site, but the airport still favours an underground station at the facility.
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 rail 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."
But the airport welcomed the planned construction of an extra station in Keilor East, which would be built as part of the rail link project.
It would also include a rail bridge over the M80 Freeway, 12 kilometres of extra track and an upgrade to nearby Sunshine station, according to a report published in The Age newspaper.
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