The $837 million cost blowout for state taxpayers was announced in late September but the Allan Labor government did not detail where it would find the extra cash.
Treasurer Tim Pallas on Wednesday confirmed it would come out of the state's consolidated fund, its primary financial account, but the money is yet to be accounted for.
"To the extent that this is additional expense on the ledger, it will have an impact around the state's debt position unless, of course, I can find offsetting value for the state," he told reporters.
"That's exactly what I'm looking for at the moment."
Tim Pallas' ninth state budget forecast Victoria's net debt would hit $187.8 billion by mid-2028. (Joel Carrett/AAP PHOTOS)
The Metro Tunnel was originally costed at $10.9 billion when it was first announced in the 2016 state budget, but several escalations have pushed the price tag for taxpayers to $13.48 billion.
The project features five new underground stations and will connect the busy Sunbury, Cranbourne and Pakenham lines through a new tunnel when it opens in 2025.
Mr Pallas flagged taxpayers would have to wait until either the mid-year budget update or 2025/26 budget to learn how he would square the ledger.
The government is thinking "creatively" to fill the funding hole but the treasurer signalled a new tax wasn't on his radar.
"We don't anticipate that we'll be able to do much in the space of taxes, given the budget before last was substantial," Mr Pallas said.
"Whilst I'm not ruling out adjusting the tax (settings), we've reduced or removed some 64 taxes in the state in the 10 years that I've been treasurer."
The May state budget, Mr Pallas' ninth as treasurer, forecast the state's net debt would hit $187.8 billion by mid-2028, pushing up annual interest expenses to $9.4 billion.
In June, a report from Auditor-General Andrew Greaves revealed there was insufficient contingency funds remaining to address issues and finish the tunnel.
With contingencies exhausted, Opposition Leader John Pesutto questioned where the treasurer would find the money.
"Don't believe Tim Pallas when he says they won't tax more, Labor has it in their DNA to tax more," he said.
In addition, the Victorian Liberal leader wants to put Melbourne's axed East West Link back on the state's infrastructure agenda as the coalition continue to attack Labor's pet project, the Suburban Rail Loop.
"At some point the East West Link does need to be built," he said.
Ex-premier Daniel Andrews controversially ripped up a contract signed by the former coalition government to build the contentious road project after Labor won the 2014 state election.
Victoria's auditor-general later revealed the total cost of scrapping East West Link topped $1.1 billion, including a $642 million termination settlement.
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