Chief Health Officer Brett Sutton says its "likely" the virus has already spread beyond Shepparton, where there are now 21 cases associated with three families who have children at three local schools.

All regional centres entered a new lockdown at 1pm on Saturday. It won't lift until 11.59pm on September 2 under the best case scenario.

However, regional communities have been spared the curfew imposed on the capital.

Premier Daniel Andrews told Victorians he had no choice but to impose some of the harshest restrictions the state has seen to ward off a crisis on the scale NSW is facing.

Access to child care centres has been shut down for all but vulnerable children, and the children of authorised workers.

Authorised workers will need to obtain permits to go to their jobs from 11.59pm on Monday.

There'll be more workforce limits and mandatory testing for high-risk industries in Melbourne, such as abattoirs, meat processing centres, and supermarket distribution centres.

Masks are now being recommended for primary school students when they are indoors, to address a significant over-representation of young children among the state's 402 active cases.

Mr Andrews also wants students aged 12 and over to have had at least one dose of vaccine by the end of the school year.

He says he fears what could happen if such a large, unprotected group begins moving around the state and country over the Christmas holidays.

"In terms of age profiles a quarter of our cases are under the age of 10," COVID-19 Commander Jeroen Weimar told reporters.

"44 per cent of our cases are under the age of 20, half of our cases are aged between 20 and 60, and only four per cent are over the age of 60," he said.

Victoria officially recorded 61 new locally acquired cases on Saturday, including 39 that were infectious in the community. Authorities have only been able to link 48 of them to known outbreaks.

There are deep concerns about unlinked infections across a wide area of Melbourne including Airport West, Frankston, Keysborough, Docklands and Yarraville.

An additional 16 cases will be included in Sunday's official count - all of them in Shepparton and detected through rapid testing after the city's first positive case was reported on Friday.

Late on Saturday, the Goulburn Valley Health service said further rapid testing had added a further four cases to the Shepparton tally, taking the cluster to 21.

St Mel's Primary School, Orrvale Primary School and the Greater Shepparton Secondary College (GSSC) have been deemed tier-one exposure sites, and students and staff have been ordered to isolate and get tested immediately.

The Goulburn Valley Health service has said the danger period includes the entire school week, dating back to Monday.

The other major cluster of concern is the MyCentre Multicultural Youth Centre at Broadmeadows in suburban Melbourne. Another 14 cases reported on Saturday, have taken that total to 27.

Mr Weimar said it was still possible to ward off a crisis on the scale of NSW, where 825 new local cases and three deaths were reported on Saturday.

"We need six million people to do the right thing, we can't do it on our own. We can't let go of the rope," he said.

Statewide almost 9000 primary close contacts and more than 10,000 secondary contacts are in isolation to help contain the virus.

Mr Andrews said the child care shutdown would be tough for many families, but given how many centres are now exposure sites, it was an essential decision.

"Many, many young people get this and we can't be certain what that means for them now, or in the future. We have to protect them," the premier said.

Australian Associated Press