V/Line's chief executive Theo Taifalos has resigned after the system was plagued by mass cancellations and delays for the past three weeks.

Key points: V/Line CEO Theo Taifalos has resigned

V/Line CEO Theo Taifalos has resigned System plagued with problems with carriage wheels and boom gate faults

System plagued with problems with carriage wheels and boom gate faults Free travel has been extended until February 7

The Victorian Government confirmed Mr Taifalos tendered his resignation and will be replaced by Public Transport Victoria's interim CEO Gary Liddle.

Mr Taifalos said he tendered his resignation to V/Line chair Jenny Dawson on Wednesday night.

He said they both believed the organisation would be best served by a new leader.

"I am grateful for the almost three years I have spent at V/Line, leading a very passionate team through a time of unprecedented growth," he said in a statement.

"Together we have transformed V/Line into an organisation focused on safety and customers.

"I wish the V/Line team all the best as they continue on this journey of change."

Victorian Transport Minister Jacinta Allan said Mr Taifalos was not forced out.

But she said she had made it clear that the Government "did have some concerns about the operational capacity within V/Line".

"It's an organisation that has some challenges ... I spoke to the board and the board is undertaking an independent review into the capacity of the organisation," she said.

"In that period between last week and this week, clearly the now former CEO reflected on his position and has chosen to resign."

Permanent solution to V/Line boom gate problem to take months

Ms Allan said she had been misled about the extent of the network's problems, which are now expected to drag on for several more weeks.

"It was clear that we were not given the best possible advice, and obviously in Government you rely on the advice of your operators, your technical experts to make decisions," she said.

"Particularly too when you're informing passengers about the level of service they can and and should expect to go about their daily lives — particularly when it comes to the regional service when they rely on it so much to get to work in the city, to make those important medical appointments — they deserve to have the best and the most up-to-date information as much as the Government does."

But Opposition Leader Matthew Guy said the buck stopped with the Government.

"The Minister is blaming everyone else except herself, she should seriously be considering her own position rather than scapegoating others," he said.

Free V/Line travel extended into Febuary

Ms Allan said problems with V-locity trains not setting off boom gates in the Gippsland corridor would continue for several weeks.

"The interim solution that is being worked on right now is expected to take up to six weeks, because it's a solution that needs to be put on 21 of the level crossings along that line," she said.

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She said the Government would accelerate funding for a permanent solution, which involved installing axel counters at the 21 locations, and would "hopefully take three to six months".

Ms Allan apologised for the disruptions and offered passengers an extra week of free train travel.

Commuters will now travel free until the last service on Sunday February 7.

Customers using Myki money will not have to touch on during that period, and Myki passholders will receive an automatic reimbursement equivalent to the 16 days free travel being provided, V/Line said.

However the free travel does not extend regional town bus services.

Since Saturday, V/Line has been running free train and coach services for commuters to compensate for the mass cancellations of services.

In a statement, V/Line said they had accelerated their maintenance program and had "crews working around the clock to return services to normal as quickly as possible".