Travel permits return to the border from midnight Friday, even though Victorian officials say the health measure isn't aimed at those communities.
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Victorian Health Department deputy secretary Jeroen Weimar said he was "very aware" of the challenges already faced by border residents this year.
"This is not intended to limit or inhibit their movements; we do ask them to go online at midnight tonight to download that permit and allow for easy travel across," he said on Friday.
"We are not concerned about rural NSW, we are not concerned about those border communities, we are concerned about those (hot spot) residents."
Victoria Police was contacted for details of how the permits, available via the Service Victoria website from midnight, would be checked.
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The state's Chief Health Officer Brett Sutton said people should expect delays at any road checkpoints, which would not be right on the border "for obvious reasons".
"The border communities have significant numbers of people moving across but are really only moving across from areas right next to the border," he said.
Permits were announced about 90 minutes after NSW Premier Gladys Berejiklian reported NSW had 28 coronavirus cases, a rise of 10 in the past 24 hours.
Dr Sutton expected it would take several weeks to control the outbreak.
Under the new system, people from the Northern Beaches area are not allowed to enter Victoria while those from Greater Sydney need to be tested and self-quarantine until they receive a negative result.
People travelling from regional NSW are asked to monitor for symptoms.
Dr Sutton said while the situation in Sydney, while concerning, had some reassuring elements.
"The places of transmission have been identified and the appropriate individuals have been followed up," he said.
"What we don't have is a number of unknown or mystery cases."
Victorian Health Minister Martin Foley said Sydney cluster should send a message to Victorians.
"This is not over, we need to make sure that to stay open, to stay safe, we still need to follow the rules," Mr Foley said.
"I hope the permit system is working properly tonight as it will be under extreme pressure over the next week as regional families look to spend time together," he said on Friday afternoon.
