More than 31,000 permits to enter Victoria have been approved since the state launched its new "traffic light" system some three hours after border changes came into effect.
The permit system wasn't available on the Services Victoria website until about 8.55pm on Monday - despite the changes happening at 6pm.
Among them was the introduction of a $4957 fine for those arriving without a permit.
Emergency Services Minister Lisa Neville on Tuesday apologised to Victorians who were unable to apply for a travel permit, describing the delay as "terrible".
"There were technical issues of trying to get this set up properly, with Services Victoria working through some of the glitches to make sure it was working properly before it went online," Ms Neville told reporters.
"A number of people absolutely were inconvenienced, frustrated and probably quite anxious as a result of that. I thank them for their patience and apologise for what happened."
She confirmed no-one was fined as a result of the delays.
"It is now working very, very smoothly; 31,000 people applied and have got a permit," Ms Neville said, adding it takes about five minutes to apply.
Under the system, regional NSW became an "orange" zone, meaning stranded Victorians can come home if they apply for a permit and get tested for COVID-19 with 72 hours of their return.
Greater Sydney and Greater Brisbane, however, remain "red" zones.
Opposition Leader Michael O'Brien described the delay as a "complete debacle".
"If you can't run a website, how can you run a state?" he said.
"Maybe we should look at fining government ministers $5000 every time they stuff up."
It comes as authorities prepare for the arrival of 1200 tennis players, officials and support staff on Thursday ahead of the Australian Open, which begins on February 8.
Ms Neville said all players and staff will quarantine at one of three hotels for two weeks.
Players and one support person, such as a coach or physiotherapist, will be permitted to leave their hotel rooms for training and treatment. They will be tested daily for COVID-19.
If a player or staff test positive for the virus, they will be transferred to a medi-hotel.
Ms Neville said the program was being funded by Tennis Australia and had been signed off by the chief health officer.
"We have put in place the strongest and strictest rules that apply for tennis across the world," Ms Neville said.
Victoria has recorded no new local or interstate-acquired coronavirus cases for the sixth day in a row, after receiving 18,139 test results.
There have also been no new cases recorded in hotel quarantine.
There are 38 active cases of COVID-19 in the state, down from 40 on Monday.