Public transport workers who shut down the rail system for several hours on Friday have been encouraged to use the threat of cancellations during the AFL finals as a bargaining chip in their pay battle with Metro.

Saturday will be the third straight day in which trains will stop due to industrial action that is part of a fierce dispute between Metro and the Rail, Tram and Bus Union over workplace conditions.

At least 70 early morning Saturday services have been cancelled, including a handful of the last services out of Flinders Street Station on Friday night, because of a four-hour stoppage to be held between 2am and 6am.

It follows the cancellation of 689 trains on Friday, disrupting an estimated 300,000 trips, and 18 early morning train cancellations on Thursday due to a one-hour stoppage.

Friday's rail stoppage caused less transport chaos than had been feared. VicRoads said traffic congestion was hardly any worse than a normal work day after the authority cancelled road works and encouraged workers to avoid travel if possible.

Public Transport Victoria also said the city generally coped well, even though most trains between 8.30am and 3.30pm were cancelled.

Rail, Tram and Bus Union state secretary Luba Grigorovitch warned Metro that the union was prepared for a long battle to protect existing conditions.

"Members of the Rail, Tram and Bus Union realise it's not a sprint, it's a marathon," Ms Grigorovitch said at a midday rally of hundreds of union members at Flinders Street Station.

A second four-hour tram strike is planned for Thursday as part of the union's negotiations with Yarra Trams.

The Victorian union movement has rallied around the RTBU after it was harshly criticised by the Andrews government for shutting down Melbourne's rail and tram networks while negotiations for new enterprise agreements were progressing.

John Setka, CFMEU state secretary, encouraged striking workers to use finals fever to their advantage against Metro and Yarra Trams.

"It's finals time soon, what a wonderful time to have an industrial campaign," Mr Setka told the rally.

He also warned the government it could regret throwing its weight behind Metro's cause in the dispute.

"This is my message to the government: be wary and be careful of where you step and what you say and what you do, because a lot of this comes back and haunts you," Mr Setka said.

"They've only been in power not even a year and it was unions like the RTBU that campaigned for this government and they were full of promises to make this a decent state for workers and look what they've already done."

Public Transport Minister Jacinta Allan was unrepentant about the government's position and said the strike action had affected the local economy.

"Not everyone has the chance to choose to work from home or take a day off," Ms Allan said.

"Some people are just going to be in the situation where they have to lose a day's pay because they haven't been able to get to work today, and they're the people who have every reason to feel angry and fed up with this action that's been taken."

Among conditions the union is fighting for are limitations on the number of times a train driver can run up and back on the same line, and how much flexibility Metro has to set driver rosters.

Metro argues the rail network must be split into five groups, and drivers restricted to one group, for it to run a more reliable system.

With Benjamin Preiss