The train was forced to make a stop at Marla, 970km northwest of Adelaide, on Thursday.
Thirty-two guests from Greater Melbourne and Bendigo, who boarded the Ghan on Wednesday, were taken off the train and put on a bus back to Adelaide.
Journey Beyond, the operator of the iconic outback rail service, said it would ensure the group was provided overnight accommodation upon arrival.
“Effected guests on the south-bound Ghan Expedition who disembarked in Alice Springs and those on the Indian Pacific disembarking in Adelaide will also be accommodated overnight,” it said in a statement.
“We appreciate our guests’ experience have been significantly impacted through no fault of their own, or ours, and we are working to help manage their individual circumstances as best as possible.”
South Australia Chief Public Health Officer Nicola Spurrier said a number of passengers had been at high-risk exposure sites in Victoria.
It comes as more than 25 domestic flights out of Melbourne have been cancelled as states and territories close their borders to Victoria over the growing Whittlesea cluster.
Melbourne Airport was still busy as many travellers made a mad dash to catch the last flights out of the state before the seven-day lockdown begins just before midnight on Thursday.
Virgin Australia pre-emptively cancelled more than 10 services in and out of Melbourne prior to the shutdown being confirmed.
The carrier has been inundated with calls and is asking customers who are not travelling in the next 72 hours to call back later.
Virgin said it would directly contact any customers impacted by changes to flights due to lockdown, including Melbourne services.
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