Metro Trains has been ordered to issue a refund to every Melbourne commuter who touched on during Thursday's "unacceptable" peak hour chaos, with the operator also facing penalties.
A computer glitch shut down the entire network at about 4pm, leaving thousands of passengers stranded for up to two hours on trains and platforms.
Victorian Premier Daniel Andrews said the shutdown was "completely unacceptable".
"Anyone who touched on during that period of time yesterday will receive a refund and we've told Metro Trains to get that done as soon and as easily as possible," Mr Andrews said in a statement on Friday.
"We have demanded a comprehensive investigation into what happened, because there must be accountability and there must be consequences."
Public Transport Victoria chief executive Jeroen Weimar says engineers traced the problem to one server in the Metro control room, and the organisation will be "relentless" in trying to understand the cause.
Public Transport Minister Jacinta Allan said the contract with Metro Trains allowed for penalties to be applied.
"We expect a higher performance standard under the next round of contracts for Metropolitan trains and trams," Ms Allan said.
Metro chief executive Mike Houghton said he expected to be hit with a penalty.
"The hit we had yesterday is a very large hit on our performance bonus," he told the ABC.
Ms Allan also took aim at ride-share company Uber, whose prices skyrocketed at the height of the chaos.
"I think their (Uber's) behaviour yesterday exposed their approach to people," Ms Allan said.
An Uber spokesman said prices spiked but levelled off as more drivers went online to meet demand.
"This resulted in thousands of Melburnian commuters being able to get home to commitments they otherwise would have missed with an average wait time under six minutes," he told AAP.
Opposition public transport spokesman David Hodgett said the refund to Myki cards doesn't go far enough.
"Who's going to the pay the compensation for the mums and dads that had to jump in a taxi or an Uber and get charged $100 to get to the childcare centre to pick up the kids?" Mr Hodgett told reporters.