More than 31,000 people have applied for the Victorian government's new border entry permits since applications became available.
The permits were due to be available on the Service Victoria website at 6pm, aligning with Victorians locked out of the state being able to return, but the website was not ready.
Michael Kent and Carly Wladkowski, of Melbourne, who had been waiting in self-isolation at Mantra for their exemption to be approved by DHHS after attending an Albury funeral, were able to secure their permit at 9pm.
There was no delay for them crossing at the Lincoln Causeway checkpoint.
Victorian Emergency Services Minister Lisa Neville apologised for the delays but disputed the shortfall was a trend after issues with applications for a travel voucher system.
"There was a glitch. Unfortunately, that does happen with IT systems," she said.
"It's now working very, very smoothly. 31,000 people applied and have got their permits. And the system is now working at five minutes per person.
"My apologies to anyone who was frustrated and held up. There were no fines issued."
Michael Kent and Carly Wladkowski were among people seeking to enter Victoria who were released from self-isolation, after testing negative.
Ms Neville said there were others in official hotel quarantine accommodation who were also being released.
"We don't want anyone in there who doesn't need to be in there," she said.
"[We had] exemptions that enabled people from the fourth of January to start leaving, and then we've changed to permit system which also changes the arrangements for people as well.
"Since the fourth of January, we've had 250 people, domestic people, who have left hotel quarantine and yesterday, 62 were able to leave."
But Ms Neville, addressing the media about the Australian Open, could not say if the border would be open in time for the event.
"I can't predict where we'll be at that particular point on the 8th of February when the tournament commences," she said.
"There's no doubt that the pandemic ... has had an impact on all our events.
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"What we're trying to do now is to protect what we've done.
"I think this is very much going to be a day-by-day situation and assessment about, you know, what the numbers are in New South Wales, where the spread is, is that linked to outbreaks?
"It will be up to the Chief Health Officer to determine when it's safe to enable people to come back from Sydney."