The project has a forecast $364 million overspend on its tunnels and stations, according to the Victorian Auditor-General's Office report tabled on Wednesday.
However, that amount is offset by savings and descoped works in other areas of the project.
About three years out from its completion date of 2025, Rail Projects Victoria has spent or allocated almost all the tunnel's $740 million in risk contingency funds.
The audit put that down to unplanned costs and "risk events", with the lack of any more contingency funds a significant budget risk.
"To stay within the project's approved budget of $12.58 billion and meet the September 2024 internal target opening date, Rail Projects Victoria needs to diligently manage the project's emerging risks," the report reads.
RPV advised the government in May this year it would likely need further funding in the two financial years after 2023 to deliver the full scope of the project and deal with potential contingency costs, the audit said.
At the time of the audit, RPV had not sought the extra money.
A recommendation to review the project's budget from the bottom up and determine how much more cash it might need has been accepted by the government.
There have been 33 scoping variations during the project's main construction phase, including the removal of a high-capacity signalling system.
The change cuts about 27 kilometres of new signalling technology, or one-third of the previously announced coverage, freeing up $91 million to redirect to other areas.
Wider "network enhancements" have allowed the government to reallocate $236 million to offset overspends in various areas.
The advent of plans to build a Melbourne Airport Rail line was another example of Metro Tunnel descoping, Rail Projects Victoria deputy CEO Peter Wilkinson said.
"There would be wasted money to continue to do some of that scope that would have to be redone by the airport project," he told reporters.
The taxpayer bill for the tunnel has grown to $12.58 billion, up from $12.38 billion in the May budget, after the Victorian government agreed to pay out a $41 million COVID-19 claim to contractors.
Victoria has not been immune from global COVID-related workforce and supply chain issues, Transport Infrastructure Minister Jacinta Allan said.
"This is a project that remains facing some challenges on cost," she said.
"You can't just set aside COVID. This is something we're faced with (and) NSW reported on these matters just yesterday."
Opposition transport infrastructure spokesman Matt Bach accused Ms Allan of deceiving Victorians by attempting to shift blame for cost overruns.
"This isn't a big build - this a big bill that every single Victorian will be paying for for generations ," he said.
Along with the financial issues, the audit notes the project poses a risk to medical and scientific equipment near two of its stations due to electromagnetic interference from trains.
While there are plans to mitigate the risks, the Department of Transport and Rail Projects Victoria have agreed they should be implemented before train testing starts in June next year.
The Metro Tunnel is estimated to be completed by 2025, a year ahead of schedule.
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