Those applying online for permits to cross from Victoria into NSW have faced delays after reports the web page stopped working hours before the border closed.
The system appeared to be back up and running again before midnight, when the Victoria-NSW border officially shut.
A Service NSW spokesperson said the permit application system was experiencing high levels of demand.
"We are aware that some people have experienced delays in securing a permit and we apologise for the delay," the spokesperson said in a statement on Tuesday night.
"In the interim, travellers will be able to demonstrate their eligibility to cross the border to police by carrying relevant documentation based on a category of exemption."
Victoria and NSW agreed to shut the borders between the two states at midnight on Tuesday as the number of coronavirus cases grows in the south.
Permits are being issued for people who need to travel interstate for work or health care.
Another 191 virus cases were confirmed in Victoria on Tuesday, lifting the state's active cases to 772, an increase of 710 in four weeks.
There are 1194 active cases in Australia.