It follows a warning from Victoria's Public Transport Ombudsman that commuters must be warned before a train switches to express and starts skipping stations.

Metro on Monday conceded that some peak-hour services are switching to express and that this was "the wrong decision".

Ombudsman Janine Young said customers needed timely information to make informed decisions on whether to board a train or wait for the next one.

"If a train is going to express, an announcement will allow people to not catch that service and wait for the next one," she said.

"That's really important from a customer service perspective. We do get complaints about service delivery, cancellations, punctuality or skipping stations."

Metro said there was no "minimum warning time" for announcing to commuters a train was being changed to express, but added it tried to give as much notice as possible.

On Monday, Labor's public transport spokeswoman Jill Hennessy said that if Labor won government it would stamp out the practice.

Ms Hennessy said Metro's train punctuality figures "have been built off the back of station skipping and timetable manipulation" by the Napthine government.

She said Labor would stop Metro skipping stations and "look at introducing penalties for operators if trains skip stations without notifying commuters".

But Transport Minister Terry Mulder denied skipping stations was about trying to improve statistics around performance.

"Fatalities, sick customers, police operations, vandalised trains ... if something like that happens and you get a train out of sequence, and drivers out of sequence, you can either leave it like that for the rest of the day and disadvantage a whole range of passengers or as quickly as is possible stabilise the timetable," he said.

And he said the number of trains skipping stations was very low, about 0.5 per cent of services a week.

In the 12 months to August, Metro altered 2421 services to run express out of 738,896 services.

If a train service is switched to run express, it counts as a "partial cancellation" and contributes to Metro's delivery performance result.

Greens MP Greg Barber said Metro needed to say whether they were skipping stations during morning and afternon peak hours. "I've had a lot of calls from constituents who say they feel like the train has been hijacked," he said.

Terry Sheedy, state president of the Rail Tram and Bus Union, said Metro was instructing its train drivers to skip stations more and more. "It's happening every day so they can get their trains back on time and don't get fined," he said.

Mr Sheedy said Metro's estimate that it only affected 0.5 per cent of services each week was "blatant lies".

Metro spokeswoman Larisa Tait said altering a service to run express was only used to assist when recovering from a major disruption, or to avoid a knock-on effect that would ultimately lead to a major delay.

"When we alter a service, we ensure that our drivers and station staff are made aware of the changes to make announcements, and aim to express services running in the off-peak direction, impacting only the minority of customers," she said.

She said a Metro review into the practice of altering services had revealed some services were "expressed" in the peak direction. "We concede that on these occasions the wrong decision has been made and we apologise to our customers who have been affected by this.

"We heavily monitor how often and which services are altered to run express, and resort to the practice as infrequently as possible. We understand this approach inconveniences some of our customers, but our aim is to ensure the majority get to their destination on time, while delaying the smallest number of customers possible."

Public Transport Users Association president Tony Morton said it was clear Melbourne had a problem with its rail system if it had to resort to stopping patterns "being altered on the fly".

"Whether it is a perverse consequence of the way we have written the incentives in the contracts with private operators because we have a privatised system or whether we just don't seem to be as good at running trains on time as other cities around the world, for some reason we do seem to have this problem."

with Richard Willingham