Services ground to a halt from 3am to 7am on Thursday as Rail, Train and Bus Union (RTBU) members took protected industrial action to fight for better pay and job security.
More than 200 coaches were used to replace the 80 train services cancelled in the morning, V/Line boss Matt Carrick said on Thursday.
An average of 16,000 commuters would usually use the service on a Thursday but only a quarter made the trip after passengers were urged to work from home or make alternative travel arrangements.
"These disruptions are incredibly frustrating for passengers and we share that frustration," Mr Carrick said.
"Services are largely back to full capacity and normal running so that means that we're not anticipating problems for the afternoon."
Metropolitan, freight and the Sydney-Melbourne XPT train services were unaffected by the industrial action.
V/Line chief executive Matt Carrick says train services are back to full capacity. (Joel Carrett/AAP PHOTOS)
The union and transport corporation have been locked in protracted contract negotiations for seven months.
The decision to strike was not taken lightly, RTBU Victorian secretary Vik Sharma said on Thursday.
"Our members felt that V/Line is not listening to them and this is the only language they understand," he said.
V/Line workers are concerned the introduction of a new ticketing system would result in job losses and wanted job security enshrined in the agreement, the union boss said.
Workers are also after pay rises and more annual leave.
Union secretary Vik Sharma said members felt they weren't being listened to by V/Line. (Diego Fedele/AAP PHOTOS)
The V/Line boss said the corporation was looking to expand its workforce, insisting no jobs were at risk.
He said V/Line was committed to genuine dialogue and discussions to reach a compromise solution that's good for everyone.Â
"The best way forward is talks and compromise rather than strikes and threats," Mr Carrick said.
Mr Sharma said the union is still willing to negotiate.
"But V/Line cannot continue to ignore the reasonable demands of their workers for decent conditions and job security," he said.
Mr Sharma added it was time the state government stepped in to end the dispute or face the prospect of more disruption.
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