A computer glitch has been blamed after pre-dawn replacement buses failed to arrive at Wendouree and Ballarat station on Monday morning.
Some commuters arrived 90 minutes earlier than usual, before 4.40am, to wait in the cold for a bus that didn't show up.
The scheduled 4.42am bus from Wendouree to Southern Cross Station in Melbourne did not arrive because of a computer system fault, which meant coaches and drivers were not scheduled, according to V/Line.
Ballarat rail line: Southern Cross upgrades will mean coach changes, delays
Commuters had to wait for half an hour for the first train at 5.15am - this was a Melton service, where people would then be transferred to buses to continue their journey to the city.
Lorraine Williams said she usually has to be in the city before 7.30am, and usually takes the 6.09am train.
She got up extra early to make sure she would miss peak hour traffic and get to work in the city on time.
"About 20 of us were waiting at Wendouree and the bus never came," she said.
"When I phoned (Public Transport Victoria) to ask what happened, and I was told there wasn't any bus and it wasn't on their timetable - I said it was on the timetable I have."
The temporary timetable available online lists a 4.42am bus leaving Wendouree and stopping at Ballarat before running express to Southern Cross, and a second 4.55am train express from Ballarat to Southern Cross.
She said staff attempted to arrange taxis for the early morning commuters, but the train arrived first.
On Twitter, V/Line apologised to commuters and said an investigation is under way.
Hi Dallas, we were made aware of this unfortunate inconvenience and we do apologise for the mix up. We are investigating what happened and will be in place to provide the service tomorrow morning. Thank you for taking the time to contact us.— V/Line Ballarat Line (@vline_ballarat) October 20, 2019
Some passengers were able to complete their journey via taxi, however due to the availability of alternative services at this time of day, it was fastest for most passengers to wait until the departure of the first train service at 5.15am between Wendouree and Melton, which connected with coaches arriving into Melbourne at approximately 7.03am.
Passengers delayed more than 60 minutes over the time displayed for their service on the temporary timetable are eligible for compensation.
A spokesperson said in a statement the fault had been addressed, and the early buses - the 4.42am from Wendouree, the 4.55am from Ballarat, and the 5.28am from Ballan - will operate from Tuesday morning.
"V/Line apologises to passengers who were planning to catch the three early morning coaches which were unable to operate on Monday," the spokesperson said.
The incident follows the omission of the 5.50pm bus from Southern Cross to Ballarat from the temporary timetable last week.
The temporary disruption will last until Thursday, as work to upgrade Southern Cross Station's regional platform is completed.
While there are some express buses to and from Ballarat, the majority of services are buses from Southern Cross to Melton, with commuters transferring to a train from there.
The line will be closed again for three weeks, beginning November 9, to commission the new Ballarat Line Upgrade - as well as rebuilt and upgraded stations, new track has been installed to create passing loops which will be tested before passengers can return.
The V/Line spokesperson did not answer a question on whether there would be free travel during the line closure.
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