Melbourne's new train operator is investigating a spate of cancellations on the company's first morning in charge.

Metro took over the rail network from Connex at 3:00am, running its first service from Frankston, just before 4:30am.

Metro chief executive, Andrew Lezala, says they have had too many cancellations this morning and staff are trying to fix the problems.

"Most of those are rolling stock-related faults, so reliability faults with the rolling stock," he said.

"So clearly we've got a lot of work to do to address those and put some long-term fixes in place."

The Premier, John Brumby, says he expects the new transport operators to run a more punctual and reliable system, but says it will not happen overnight.

"They'll happen over the course of the next few months and the next few years," he said.

"I am very confident that you are going to see steady and continuous improvement in the way in which our public transport system operates in our state."

The new tram operator, KDR has pledged to improve service as well.

Company spokesman Colin Tyrus says all tram services will be reviewed, to ensure they have the largest capacity trams where they are needed most.

"We do have a fleet of more than 100 high-capacity low-floor trams already out of our total fleet, so we'll deploy them to the areas they're most needed."

"What we'll be doing is improving our services to customers. There will be no cutbacks," he said.

The State Opposition says the new train and tram operators face huge problems.

The Opposition's transport spokesman, Terry Mulder, says a change of uniform and a coat of paint is not going to fix the problems that we have with infrastructure.

"They've got one hell of a job ahead of them. I wish them luck," he said.

"I'd just say to the commuters. The system out there at the moment, these people don't own it, they've inherited it."

"But it is up to the Brumby Government to provide these operators with what they need to run the system," he said.