Mr Shorten, who was the federal Labor leader between 2013 and 2019, said states and territories cannot continue to lockdown forever and Australia must learn to live with the virus.
His comments come after Western Australia's Labor Premier Mark McGowan and Queensland's Labor Premier Annastacia Palaszczuk indicated a reluctance to open up even when vaccine targets are met.
"I think sooner or later some of the premiers who've been successful in keeping their jurisdictions at COVID-zero, we can't keep locking down. So you've got to accept COVID in the community," Mr Shorten said in an interview with Steve Price on Tuesday.
"What we've got to do is use this period of lockdowns to COVID-proof ourselves as best we can to minimise the lethality, the harm that's caused by COVID.
"But at a certain point, we will have to learn to live with it."
National Cabinet in recent weeks agreed to Australia's pathway out of the pandemic, based on a report provided by the Doherty Institute.
Australia will move from the suppression phase to Phase B when 70 per cent of those aged over 16 are fully vaccinated and Phase C when 80 per cent receive their two jabs.
At Phase C, there will be minimal restrictions and highly targeted lockdowns only.
Prime Minister Scott Morrison on Monday said Australia must start "coming out of the cave" and live with COVID-19 like other infectious diseases when the vaccine targets are achieved.
"Once you get to 70 per cent of your country that is eligible for the vaccine and 80 per cent, the plan sets out that we have to move forward," he said.
"We cannot hold back. Our task between that day and now is to ensure that we ready ourselves for that next phase."
New South Wales Premier Gladys Berejiklian said "every state will have to live with COVID" and declared the Delta strain cannot be kept out of other states and territories forever.
But Mr McGowan, who said he will continue to pursue a zero-COVID-19 approach, noted the Doherty Institute report still allowed for lockdowns at Phase B and Phase C.
"It's in black and white. People should read the plan," he said.
"My view is we should do everything we can to stay in the state we are currently in, and at the same time vaccinate like hell.
"I think that's the majority view here and in the states without COVID cases. And in Victoria and the ACT, which are trying to eliminate it as we speak."
Ms Palaszczuk on Tuesday said the Doherty Institute report "was all predicated on 30 cases across Australia, not 13,000".
She has insisted on seeing updated modelling from the Doherty Institute, due to be released on Friday, and has not ruled out keeping the border closed with NSW if case numbers remain high at Phase C.
"At the moment the borders are shut and, you know, we don't know when they're going to come out of their current outbreak," she said.
Mr Shorten said it was still possible for Mr Morrison to get state and territory leaders on the same page.
"I don't think it helps when Mr Morrison says, you know, the premiers must do this and that by Friday," he said.
"I mean, it may sound good and it may be red meat to your base, but in life, if you're going to persuade people, don't kick their heads first. You know that just sort of gets people's backs up."
Mr Shorten also told The Australian he thought the 80 per cent vaccine target set by the Doherty Institute was acceptable but wanted youngsters protected as well as adults.
"To open safely, it's about reaching high enough vaccine coverage plus focusing on other measures such as adequate ventilation, masks, third booster doses for health workers, and vaccinating children," he said.