Border controls have caused major disruptions to public transport with coaches replacing trains and travellers needing to find their own way interstate.
V/Line advised on December 31 that from New Years Day, no V/Line trains would run to Albury.
"All Albury train services towards Melbourne will originate at Wodonga (not Albury).
"Passengers who are permitted to travel from Albury should make their way to Wodonga station to board the train.
"The shuttle coach between Albury and Wodonga will no longer operate. These changes will remain in place until further notice."
However, 10 services that were due to run on the Seymour line have been replaced by coaches since January 1.
The 7.05am service from Melbourne on Tuesday arrived at Wodonga station shortly before 11am.
Meredith Ward took the coach from Southern Cross and said she only found out that morning it would not run as a train.
"As far as I knew it was going to be a train, and then I got there and there were all these people around in vests telling everyone it would be replaced by a coach," she said.
"There was a lot of confusion and a lot of disgruntlement, the staff in Melbourne said it was arranged at 5 o'clock this morning.
"I'm not quite sure why there was a sudden change."
Ms Ward said she was only bound for Wodonga for a meeting and to stay with friends, so did not require a permit, but others were unsure how they would get to Albury.
"Everyone was told you'll have to make your own way to Albury," she said.
"People were discussing getting a train or a taxi.
"They were just kind of left high and dry, trying to make arrangements on the spot."
Ms Ward said terminating the service at Wodonga seemed unnecessary.
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"You've got to get a permit to come back in ... it's absolutely over the top," she said.
Establishing staff arrangements were the reason some trains on Monday and Tuesday were replaced by coaches while V/Line worked through complex rostering requirements.
"We have been working closely with DHHS to set up the appropriate arrangements for transport staff to cross the border safely in line with the previous border closure. We thank passengers for their patience," a V/Line spokesman said.
"All passengers are reminded to ensure they wear a mask on public transport and inside stations, practice good hygiene and not to travel if they are feeling unwell."
Albury trains will resume running to and from Melbourne on Tuesday 5 January for the evening services.
A NSW TrainLink bus appeared to be taking passengers from the V/Line service.
Passengers originating from NSW are also being left to arrange travel on a state-by-state basis with the Sydney to Melbourne XPT service terminating at Albury.
"From 2 January 2021, the NSW-VIC border will remain closed until further notice. For travel beyond Albury please organise alternative arrangements for your onward journey," is the travel advice.