Some Ballarat passengers were delayed by more than two hours as V/Line rushed to replace train services cancelled due to a landslide beside tracks east of Bacchus Marsh and signalling problems at Sunshine.

V/Line spokesman Daniel Maloney said rail services were cancelled in both directions between Ballarat and Melbourne.

He said four of Victoria's five regional train lines and a number of metropolitan lines were closed following yesterday afternoon's deluge, forcing a mad scramble for every available coach to transport passengers.

"Delays have been significant, at least one hour and quite possibly two or more hours," Mr Maloney said.

"It took at least an hour for the first wave of buses to come in, we were calling coaches in to go in all directions with four country train lines and a few metro lines closed, there were many thousands of people being moved by bus.

"It was not helped by the fact roads were suffering as well and the city area was completely congested."

Mr Maloney said the line between Melbourne and Ballarat was closed from 4pm and coach services were scheduled to replace train services until midnight last night.

He said while some passengers were understandably disgruntled, "98 per cent" were understanding of the situation.

Napoleons resident Ann Sissens arrived back in Ballarat an hour late in the first wave of coaches, after the 4.05pm train was among the first cancelled.

"Most people were okay about it all. There were lots of delays but the staff were very good," she said.

"You could see how much rain there was as we came through Bacchus Marsh, all the vegetable growing areas were just flooded."

From Ballarat, a group of Ballarat Grammar School students were provided with a taxi home to Bacchus Marsh, after being unable to fit on the replacement coach service.

Mr Maloney said while Vline would be endeavouring to return as many trains as possible to Ballarat from Melbourne overnight in time for this morning's commuter rush, further delays could be expected.

"There could be potential flow-on effects; at this stage we are expecting services to be back to normal but we may need to run additional road coaches," he said.