Metro Trains could face fines and penalties for the crippling network shutdown on Thursday evening, Public Transport Minister Jacinta Allan says.

She told reporters there were provisions in the existing contract with Metro to impose penalties and she had already held talks with public transport officials about it.

"There are mechanisms under the current contract that allow Public Transport Victoria to put a penalty on the operator," she said.

"I'll be having discussions and have been having discussions with the CEO of Transport Victoria about activating the mechanisms in the current contract."

Metro chief executive Mike Houghton said they had never had a failure like this before on a train control system and he expected they would take "a hit" in terms of penalty.

"The fines and penalties are worked out every month. It does happen every week by routine," he said.

"So the hit we had yesterday is a very large hit on our performance bonus yes."

The discussion of a possible fine comes at the same time as Metro is trying to renegotiate a contract extension.

"We do want to look at strengthening both the overall performance to make sure that these sorts of incidents don't occur regularly on the network," Ms Allan said.

Mr Houghton said commuters that touched on to use the train network between 3:00pm and 7:00pm would be reimbursed for the cost of their two-hour fare.

"Both myki money and myki pass passengers travelling on a full fare will be reimbursed $4.10 and concession travellers will receive $2.05," he said.

"These refunds will be processed automatically over the next 30 days - passengers do not need to fill out an application form."

Commuters flooded on to trams following the train chaos. ( ABC News: Chris Le Page )

Unacceptable impact on passengers

Ms Allan said she had ordered a "comprehensive investigation" into what happened, calling it "unacceptable, infuriating and frustrating".

"It does need to be recognised that this was an unacceptable impact on passengers and the investigation needs to consider that as well as what happened," she said.

Opposition transport spokesman David Hodgett described the incident as "complete chaos".

"What's the point of having a backup system if it can't come online fairly quickly and then provide information to commuters and people about what the problem is and what the alternative modes of transport are to get home," he asked.

Ms Allan said she had been asking the same question.

"There is a backup system but in this instance it failed. I've been advised that this computer system failure is unprecedented," she told 774 ABC Melbourne.

Luba Grigorovitch, the secretary of the Rail, Tram and Bus Union, said there was no backup system and one that failed has had over 1,400 faults.

"Metro haven't provided for any software or hardware backup systems. We know for a matter of fact that there's 1,400 faults with this new system that's been put in place by Metro," she said.

"The fact that there is no software or hardware backup system, no procedure or policy for managing such an event is outrageous."

In November last year, the Metro control centre near Southern Cross Station was evacuated after a false alarm, forcing the network to be shut down for 30 minutes.

Trains started running again at Nunawading station, in Melbourne's east, at about 5:00pm. ( ABC News: Kathy Lord )

'Disgraceful behaviour'

Ride-booking service Uber implemented its surge pricing policy in the wake of the transport problems, where fares automatically increase during a time of high demand, making an Uber ride even more expensive than normal.

Acting Premier James Merlino called the move "disgraceful behaviour" and said it was an example of why the Government was trying to make legislative changes so taxis and ride-booking services could compete on a level playing field.

"This was disgraceful behaviour for Uber and they should be condemned for it," Mr Merlino said.

"So in the future we will have a level playing field and people can make their choice. And I think [with] the behaviour of Uber yesterday, plenty of people will be making choices in the future and that won't include Uber."