Metro Trains is "deeply disappointed" by Melbourne's catastrophic peak hour train shutdown and will refund all customers the cost of a two hour fare as compensation.
A computer glitch shut down the entire network at about 4pm on Thursday, leaving thousands of passengers stranded for up to two hours on trains and platforms.
After scathing criticism from the premier and transport minister, Metro will refund $4.10 for full fare pass holders and $2.05 for concession users within the next 30 days.
"In recognition of the inconvenience our passengers experienced, we will be issuing an automatic refund, passengers do not need to fill out an application form," Metro CEO Mike Houghton said in a statement.
"I am personally making sure we understand every detail of what happened last night."
The refund comes after Premier Daniel Andrews vowed all passengers would be reimbursed for the "completely unacceptable" delays.
"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 expects 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.
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 didn'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.