New stations and a sky rail bridge connecting the Melbourne CBD to Tullamarine would be built as part of the multimillion dollar project originally due to be completed by 2029.
But Deputy Premier Jacinta Allan said the government was expecting to push that date back.
"It has been challenging to negotiate with the airport about how the project will be delivered on the land that they lease from the federal government," she told ABC Radio Melbourne on Monday.
"Those negotiations, particularly with the airport, have at times been a little frustrating, they've been challenging and they have put real pressure on the completion date."
The Victorian and federal governments are each contributing five billion dollars towards the project, which is expected to cost between eight and $13 billion.
In 2018, Melbourne Airport was part of a consortium offering five billion towards the project with the aim of installing a tunnel.
But with rising state debt, there have been reports the Victorian government was looking to cap spending on the rail link.
Ms Allan said the government was in discussions with the Commonwealth about the project, with governments due to hand down their budgets next month.
But she said it was the delayed negotiations with the airport that were the focus of the conversations.
"Not the budget pressure or some of the budget back and forth, which is perfectly normal," Ms Allan said.
"We've been talking to them about how the completion date is under pressure and what that means in the longer term."
The Victorian government is due to hand down its budget on May 23 while the federal budget will be delivered on May 9.
Melbourne Airport has been contacted for comment.
23°C