Mr Baillieu told reporters in Melbourne on Tuesday an audit of the system is needed to see if continuing with myki is in the best interests of Victorians.
"Obviously it's been a disaster in the terms of the cost to taxpayers and its failure to roll out successfully," he said.
"We need to have an independent look at the financials and a look at what the options are and that will obviously take some weeks.
"But we would hope to have the substantial part of this done in the next couple of months."
The new coalition government has frozen any further rollout of the myki system to V/Line regional services and retail outlets.
It has also scrapped the planned switch-off of the existing Metcard system by Easter.
The government has commissioned an unnamed major accounting firm to conduct a wide-ranging audit of the smart card's operation.
The government has also called for submissions from public transport operators and other parties.
Mr Baillieu told reporters $700 million has already been spent on the system, roughly half the cost of the myki system.
"Obviously there are costs associated with rolling it out, even as it currently is. And there are obviously costs associated with either scaling it back or scrapping it altogether, but they're the questions we want to have independently answered," he said.
"The bottom line is myki's been a financial disaster, it's been a functional disaster, there are serious questions about the Farebox, about the hand-held devices, about the functions available and indeed about its distribution and the take-up from commuters.
"We need to now make a judgment based on facts and based on information which we'll elicit through this review that's in the best interest of all Victorians."
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