Metro Trains has been fined the maximum penalty of $1.2 million after a computer glitch forced a temporary shutdown of Melbourne's train network in July.

Tens of thousands of passengers were left stranded for up to three hours on July 13 after a computer problem caused the train network to come to a standstill during peak hour.

The glitch caused 224 services to be cancelled, and 378 services to run late.

Public Transport Victoria (PTV) chief executive Jeroen Weimar said the fine represented the toughest fine it could hand out under its contract with Metro.

"This was the maximum monthly fine that we could have imposed, and rightly so, because obviously it was a major impact on the network for that period of time," he said.

"Tens of thousands of our passengers were inconvenienced and as a result we've used our contract to its full effect, and penalised them for their very poor performance."

Mr Weimar said July was Metro's worst month for meeting performance standards in five years.

The fine comes on top of the $627,000 refunded to 175,000 affected passengers.

Frustrated commuters tried to get onto packed trams after Melbourne's train lines went down. ( ABC News: Chris Le Page )

Metro is currently in negotiations with the Victorian Government to renew its contract to run Melbourne's train network.

Mr Weimar said any new contract would include even harsher penalties for failing to deliver on services.

"I think what this illustrates is that the current contract we have with Metro Trains does have teeth and does come into effect when we see these very rare, but very serious, failures in performance," he said.

"We are currently exploring future contractual options and any future contract will have even more stringent performance requirements and penalty clauses."

In July, the Government ordered an investigation into the shutdown, describing it as "unacceptable, infuriating and frustrating".

"There is a backup system but in this instance it failed. I've been advised that this computer system failure is unprecedented," Public Transport Minister Jacinta Allan said.

"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."

It was not the first time Melbourne's train network had been shutdown.

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.