Metro documents show the operator planned to cancel dozens of Friday train services due to "driver unavailability", even though just six train drivers out of hundreds called in sick.

The "planned cancellations" were booked in on a day train drivers had been planning to hold a four-hour train strike as part of industrial action, however the stoppage was called off early this week after Metro terminated negotiations with the drivers' union.

Eighteen train services are planned to be cancelled this evening, the documents show, although 12 will be in the counter-peak direction.

There was heavy disruption across the city on Friday morning due to the cancellations.

In all, more than 5 per cent of morning peak-hour trains were cancelled,  well short of the 2 per cent threshold that defines good service.

The disruption was felt hardest on some of the network's busiest lines, including the Cranbourne/Pakenham and Werribee/Williamstown lines.

Metro said fewer drivers than normal took the day off due to illness and this, combined with train and track faults, led to a total of 29 cancellations in the morning peak.

An additional 15 trains were cancelled in the morning peak due to track and train faults and ill passengers, Metro said.

"Only six drivers called in sick overnight, which is considerably less than usual, and as a result we had to cancel a small number of services," spokeswoman Sammie Black said.

"This included seven city bound services and seven outbound [counter peak] services which were spread across the network and were identified to cause the least amount of disruption for our customers."

A train driver on the Craigieburn line told commuters over the train intercom that the spate of morning cancellations occurred, despite drivers fronting up for work as normal.

"Despite all drivers turning up for work today, some were told their services were no longer required," the driver said.

The Rail, Tram and Bus Union had threatened to stop all trains between 10am and 2pm, causing chaos throughout the day.

The union rallied at Flinders Street station at noon on Friday, despite calling off planned stoppages. The rally along Swanston Street caused major delays to trams.

Union members working for Metro and Yarra Trams are locked in separate negotiations for a new pay deal, after current deals expired on June 30.

Metro abruptly cancelled talks and took the union to the Fair Work Commission this week in an attempt to have the strike cancelled.

The Andrews government also applied heavy pressure to the union to drop the planned four-hour stoppage, before the union agreed to call it off and Metro agreed to resume negotiations.

Metro offered the union a 14 per cent pay rise over four years earlier in the week, and is due to submit an "improved offer" by 5pm on Friday.

Correction: An earlier version of this story reported that 50 trains did not run due to "planned cancellations". This was incorrect. Of the 50 trains planned to be cancelled, 33 are passenger services and 17 are empty trains.