Hours before the official closure of the NSW-Victorian border comes into effect at midnight, the XPT from Sydney to Melbourne chose to terminate at Albury on Tuesday morning, refusing to go into Victoria.
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Passengers who left from Sydney at 8.40pm on Monday thought they would be on the on the overnight train for the whole journey.
But when they arrived in Albury, they were told the train would not continue south of the border.
One passenger said the announcement made on the train was "we do apologise, but the decision was made last night, last minute".
A one-off coach service, which was from Victoria, transported travellers from Albury to Southern Cross Station so they could complete their journeys.
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A Transport for NSW spokeswoman confirmed on Tuesday that the decision had been made that the XPT would not cross into Victoria while the border was closed temporarily.
"This XPT service will only operate between Albury and Central Station," she said.
"Transport for NSW and Department of Transport (Victoria) are currently assessing other public transport services which operate between NSW and Victoria.
"Transport for NSW is continuing to work closely with NSW Health, NSW Police, industry stakeholders and operational professionals around a number of important issues including freight operations, logistics and maritime.
"Special conditions will be in place for freight operations and logistics as well as other critical services. provisions will also be in place for residents of border regions, including Albury-Wodonga.
"The safety of all customers and staff is the number one priority and Transport for NSW will continue to proactively address the evolving situation."
It does not appear Service NSW will provide ongoing replacement buses for the Albury to Melbourne section of the journey.
Late on Monday, V/Line confirmed it was working closely with the Victorian and NSW governments to determine any service impacts stemming from the border closure call.
"V/Line will communicate these and any future service changes with passengers via its website, app and twitter feed as soon as they are confirmed," a statement said.
"Initially, the 6:02pm train from Southern Cross to Albury will be replaced by coaches on the evening of Monday, July 6 while future arrangements are made."
It is still unknown how the local Albury-Wodonga bus service will operate in light of border closures.
Transport NSW was still waiting for the state's public health order to be signed before making any directions on bus services.
The Dyson Group, which operates buses across both sides of the border, refused to comment when contacted by The Border Mail.