A "bureaucratic" requirement for Victorians to get tested to travel interstate has been blamed for the state system's woes, as Omicron coronavirus cases spike.
Victoria reported 1503 new COVID-19 cases on Wednesday from 92,262 test results - the most processed in a 24-hour window since the pandemic began in early 2020.
Another six people have died.
The overwhelming demand for testing forced at least 14 testing sites across the city to shut by 9.45am.
They spanned from the east at Golfers Drive in Chadstone, southeast at Peninsula Health in Frankston and north at Heidelberg Repatriation Hospital.
Some have since reopened including the drive-through at Albert Park, which suspended testing immediately after opening, for a third day in a row.
COVID-19 commander Jeroen Weimar said testing sites were exceptionally busy, with wait times of an hour to 90 minutes on average.
"The reason we suspend new people coming into testing stations is we don't want people sitting in queues for four or five hours where we can possibly avoid that," he told reporters.
Queensland, Tasmania, South Australia and the Northern Territory all require fully vaccinated Victorians to provide a negative test result to enter their states.
Mr Weimar said more than a quarter of tests in recent days had come from people needing a negative result to journey interstate, describing it as a "bureaucratic reason" why the system is jammed.
"It is not a highly productive way to use a PCR testing system," he told reporters.
"The additional queues and waiting times that we're seeing at the moment are a by-product of that. We hope to move to a more sensible arrangement in the very near future."
Despite the long queues, Mr Weimar urged anyone with symptoms to come forward for a PCR test or to use a rapid antigen test at home if they can source one from a supermarket or pharmacy.
Opposition health spokeswoman Georgie Crozier urged governments to consider using rapid testing instead for travellers.
"To have that rapid testing so that they (people) can get across the borders, I think, would be a sensible, prudent measure that governments should be looking at, at the very least," she told reporters.
Omicron variant cases have jumped to 61, up from 37 on Tuesday.
Mr Weimar said the new strain would inevitably spread further in Victoria from NSW due to the high level of movement between the two states.
Meanwhile, Premier Daniel Andrews interrupted his leave to attend Wednesday's national cabinet meeting, where Australia's leaders discussed indoor mask requirements and vaccine boosters amid rising Omicron cases across the nation.
Wearing masks indoors was highly recommended and there were no changes made to the timing between COVID-19 vaccinations, after the meeting.
If the time for boosters eventually drops to four months after a second jab, an extra million Victorians will become eligible and Mr Weimar said additional state-run sites would be set up to cater for expected demand.
More than 17,000 Victorians received a vaccine dose on Tuesday, a four-fold increase from a fortnight ago.
Victoria's active case numbers remain relatively stable at 13,888, as do hospitalisation and intensive care figures.
Australian Associated Press
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