In a press conference on Wednesday morning, Ms Allan said V/Line had not been providing an up-to-date servicing strategy since the introduction of the Regional Rail Link last June, resulting in a higher-than expected attrition rate to the wheels.

Consequently, the government has ordered that an independent review be conducted into operating problems on the V/Line network.

“I was advised late yesterday by V/Line that the cause or the reason the wheels have been wearing away and the issues that have been identified in the last couple of weeks has been the result of V/Line not adequately planning and preparing a maintenance regime to meet the needs of the services provided,” Ms Allan said.

“Disappointingly, V/Line have not put in place a changed maintenance regime to ensure that this wheel wear didn’t occur.”

The operator is carrying out additional maintenance and is replacing wheels on affected trains.

As compensation, commuters will receive free travel from this Saturday until the end of January.

Opposition public transport spokesperson David Hodgett, who was at Ballarat Station on Wednesday with Western Victoria MP Joshua Morris, said the government needs to be transparent with the service issues.

“Say this is the problem, say this is how much it’s going to cost to fix, this is how long it will take and restore services here to people at Ballarat so they can have a reliable service to and from Melbourne,” he said.

Mr Morris backed the state government’s compensation initiative, but said commuters would prefer to have a decent service returned to Ballarat.

“Certainly compensation is one thing that is duly needed as a result of these significant delays,” he said.

“However, commuters don’t want compensation in the long term – they want a reliable service that is going to get them home on time so they can see their families (earlier).”

Passengers without a ticket will be able to jump on any V/Line train or coach and not pay a cent, while pass holders who have already paid for a ticket will be eligible for a refund. 

Commuters echoed Mr Morris’ sentiments.

“In the end what people really want is for the train to run,” daily Ballarat commuter Francis Rouhan said.

The government’s review into the system will also seek an answer into a boom-gate fault.

Last week boom gates failed to lower in time for a V/Line train on the Dandenong rail corridor. The failure triggered bans for some trains. 

Ms Allan said problems with boom gates were identified in 2011 and a report was prepared for the former government in 2013.

"That report wasn't actioned," she said.

Ms Allan said she was first made aware of the recent boom gate issue on Friday evening.

Axle counters will be installed on 29 level crossings so VLocity trains can run on the metropolitan network, she said.

These devices detect the speed and direction in which trains are travelling, helping boom gates recognise the VLocity trains. Installing the devices will take three to six months at a cost of $23 million.