UPDATE 9PM: An alternative website has been launched and applications can once again me made for a border permit.
The move has come just three hours before the borders are due to close.
Applications can be made at www.disasterassistance.service.nsw.gov.au/bcpermit.
Those successful will receive their permits immediately.
The Service NSW website for Border residents to apply for a permit to cross the state line has gone down within half an hour of opening.
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.
But it was not long until the system crashed.
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".
The eligibility requirements released by the NSW government allow anyone within 50 kilometres of the border can get a permit - meaning Wodonga, Beechworth and Rutherglen residents will be successful, but those in Wangaratta and Bright will not.
The exceptions are members of Parliament, a person providing critical services, season workers, boarding school and university students and carers.
People who could get access to the system before it crashed were not given the option to choose "work" as a reason for needing the permit, but that was later rectified.