The federal government on Sunday announced its October 25 budget would include $2.2 billion for the rail loop, which Labor has promised to build but the Liberal and Nationals have vowed to ditch in order to prioritise funds for an ailing health system.
Prime Minister Anthony Albanese said the government wouldn't be open to any discussion with the Liberals about repurposing the funding if they won the state election in November.
"It's a commitment for the suburban rail loop - we make commitments to specific projects at specific times," he told reporters in Melbourne.
The Victorian opposition previously said it would write to Mr Albanese to plead its case for the money to be rerouted to health when it scrapped the rail loop.
The state's independent budget office has said building the first two sections of the loop could cost $125 billion, with the cost-benefit ratio for those parts worth 60 to 70 cents for every dollar spent.
The auditor-general also savaged the business case for the project, finding the costs outweighed the benefits.
When asked about criticism of the business case for the rail loop, federal Infrastructure Minister Catherine King said she was confident the work from her Victorian counterparts stacked up although she confirmed Infrastructure Australia was yet to properly review the project.
"There have been some challenges around that (business case), but this (funding) is for the early works of that project," she told ABC's Insiders program.
"We haven't made any further commitments and we'll talk to the Victorians around that as we go forward."
Liberal state transport infrastructure spokesman Matthew Bach said Ms King's comments threw significant doubt on the project as the federal government had only committed to initial funding.
"Given that both the Parliamentary Budget Office and the auditor-general have thrown severe doubt over the business case currently being relied upon by (Premier) Daniel Andrews, it is hard to see how Infrastructure Australia will possibly endorse the project," he said in a statement.
"Without further federal contributions, the Suburban Rail Loop has a massive black hole in its budget, meaning either more debt or higher taxes - or both - if the project is to proceed."
Earlier on Sunday, Ms King and Mr Albanese declared the end of "zombie" projects like the East West Link that the previous coalition government had kept in its budget.
The toll road project was supported by former Liberal premier Denis Napthine but canned when Mr Andrews took power.
Mr Bach accused the federal government of ripping $4 billion in funding for the East West Link away from Victoria, and said his party would work to reinstate funding to get the road project built if it won the election.
