Metro Trains is waiting to see what the Rail, Tram and Bus Union's next move will be, but says the system ran "smoothly" during a four-hour stopwork early on Saturday morning.

However, the company is bracing itself after the volatile Construction, Forestry, Mining and Energy Union state secretary John Setka​ encouraged train worker members to disrupt football finals week saying it was a "wonderful time to have an industrial campaign".

Metro Trains chief Andrew Lezala​ condemned the threat to finals commuting.

"It would be an absolute outrage if that was the case. I think it's just an absolute no-no," Mr Lezala said.

Eighty-four buses were used on Saturday to replace the 66 cancelled trains, including four late-night trains between 2am and 6am, a Metro Trains spokeswoman said.

The first train to leave in the morning was the 6.06am train from Sandringham to Flinders Street.

"Our people in the control room tell me it all ran pretty smoothly," she said.

The Fair Work Commission has granted the union a period of protected industrial action, but the union has not telegraphed its next move.

The union has not responded to attempts to contact it over the stopwork on Saturday.

On Saturday, Planning Minister Richard Wynne urged the union to continue negotiations to resolve the dispute.

"The travelling public were obviously inconvenienced on Friday. We believe that the parties should come together in the interest of the travelling public and get this matter sorted out."

Lord Mayor Robert Doyle made a "plea on behalf of the city".

"I don't think this is the way to have people have some sympathy for your cause. Enter into those discussions in good faith and get the best outcome you can. But for me I must say all this has done for me is highlight some ridiculously outdated work practices that I'd be embarrassed in trying to defend if I were the union."

On Friday, 689 trains were cancelled, disrupting 300,000 trips. On Thursday, 18 early morning services were cancelled due to a one-hour stoppage.

Melburnians affected by the strike, however, have donated more than $28,000 in fares they would have spent on their myki during the strike to Syrian refugees.

The campaign was started by Fairfield man James Wright, who was moved by photographs of the broken body of Aylan Kurdi, a three-year-old asylum seeker washed ashore in Turkey. He initially sought just $2500 in donations but now has more than 10 times that amount.

"I saw these photos and it affected me – I have two daughters," Mr Wright told Fairfax Media.

"I thought, 'surely there's something we can do in a short space of time that would make a meaningful contribution to prevent that from happening again'.

"I knew that tomorrow [Friday] was going to be very frustrating, so I wanted to channel that frustration into something useful to help people directly affected by the humanitarian crisis."

Others, unaffected by the strike have decided to contribute the money they would normally use to recharge their phone.

Supporters of the #Melbourne #trainstrike fundraiser have given many reasons for donating https://t.co/5XX1hFVmmB pic.twitter.com/Ow77YOOVzp— Australia for UNHCR (@UNrefugees) September 5, 2015

The money will go towards UNHCR, an Australian charity that raises funds to support the work of the UN Refugee Agency.

With Kate Stanton