Public transport authorities have thanked Melbourne's train commuters for "holding on" while the main toilets at the city's iconic Flinders Street Station underwent an extensive revamp.

The old toilets serving the main concourse area were the most complained about on Melbourne's train network.

Public Transport Victoria (PTV) said the lavatories were upgraded in response to passenger feedback as part of a $100-million Flinders Street Station upgrade project.

The old toilets were the most complained about on Melbourne's train network. ( Supplied: PTV )

Capacity in both the male and female toilets has been increased to reduce waiting time during busier hours.

PTV said the new facilities were cleaner and more accessible than before and would be opened today in time for the weekend's AFL matches and Open House Melbourne events.

In the coming months, the toilets at the Elizabeth Street end of the station will also be refurbished.

PTV spokesman Alan Fedda said the upgrade would bring the station, which is used by 200,000 passengers a day, back to its former glory.

"With one passenger using the toilets every six seconds during peak this will be a big relief to passengers," he said.