The Service NSW website for residents to apply for a permit to cross the state line went down within half an hour of opening on Tuesday evening.
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Anxious residents were waiting all day to ensure they could get a permit before the border closure came into effect at 12.01am Wednesday, and were finally able to get into the system at about 7.30pm on Tuesday.
Some Wodonga residents reported being able to get through the system and were quickly issued a C permit that is valid for 14 days.
"The permit may be used only for the purpose of entering NSW for work, education or daily life," the confirmation stated.
Some people were told that "this transaction is not available at this time, try again later".
Others who were already filling out their details could not get through filling it all the name, address and contact detail information before the page timed out.
Eventually at about 8pm the website came up with a new message saying "this transaction will be available soon".