Passengers on V/Line services are expected to receive compensation following days of severe disruptions.
Today is the worst day after a week of disruptions — 67 services cancelled and replaced by buses.
The government has asked the regional rail operator to come up with compensation options for commuters affected by the disruptions — such as free travel.
Last week boom gates failed to go down in time for a V/Line train on the Dandenong rail corridor, triggering bans for some trains.
Travel times for Gippsland commuters have increased significantly. Many train services have been replaced by buses.
Acting Premier James Merlino told reporters commuters had "every right" to be frustrated and annoyed.
"This is not good enough. People expect better and deserve better," he said.
Mr Merlino said investigations were taking place into the boom gate failure and V/Line would soon announce how they would fix the problem.
Wheel faults have also affected V/Line services in recent days. But Mr Merlino said maintenance had also increased to rectify the affected wheels.
"Over the course of the week services will improve."
Shadow transport minister David Hodgett said 67 trains had been replaced by "slow-running coaches" on the Ballarat, Bendigo, Geelong and Traralgon lines.
"People are angry. The system's in chaos," he said.
Mr Hodgett said passengers had put up with enormous disruptions and should be compensated.
A V/Line spokeswoman said investigations into wheel wear on the VLocity trains had continued overnight and extra maintenance shifts had been scheduled.
She said V/Line would work closely with Public Transport Victoria to look at ways customers may be compensated.
Meanwhile test drilling has begun under the Yarra River to build the Melbourne Metro Rail project.
A floating site has been set up on the river. Workers will dig 12 boreholes up to 35 metres below the riverbed to gather information about the ground conditions.
The geotechnical investigations will continue for six weeks at different points in the river.
Two tunnels will be bored underneath the Yarra and will sit about seven metres below the riverbed to make way for the rail project.
Major construction is set to begin in 2018. The government said the project will create space for an extra 20,000 passengers in peak hour.
The government has committed $4.5 billion to the $11 billion Melbourne Metro but has not yet secured federal funding.