Chief Health Officer Brett Sutton said regional Victoria is "under threat".
"It's likely with the significant movement, for essential reasons, to have gone beyond Shepparton," he said.
"That's why we have declared that all the current restrictions in Metropolitan Melbourne will apply, other than the curfew, to regional Victoria."
Restrictions will be in place until September 2.
Mr Sutton said it was a difficult day for Victoria.
"We have really significant challenges with the Delta variant," he said.
The government recommends all primary school aged children wear masks to protect themselves.
Regional Victoria has once again been plunged into lockdown.
From 1pm today, regional Victoria will be returned to lockdown in line with Melbourne but will not be subject to the curfew.
Victorian Premier Daniel Andrews said the Shepparton outbreak was 'very concerning' and there was evidence of cases travelling to other parts of regional Victoria including Bendigo.
"Sadly the public health team has advised given the Shepparton outbreak... there is a very significant risk of transmission right across Victoria," he said.
It's the first time Albury and Wodonga have both been locked down at the same time since the national lockdown from March to May 2020.
An authorised worker permit system will be introduced in regional Victoria.
A permit system is being introduce to access childcare across Victoria, with only children of essential workers and children with certain needs able to attend childcare.
IN OTHER NEWS:
48 of the cases are linked to known outbreaks, 13 are mystery cases.
It comes as 17 cases of COVID were detected in Shepparton, days after COVID fragments appeared in the town's wastewater.
The source of the infection and how it reached Shepparton is still unknown.
We have removed our paywall from our stories which contain need-to-know information about coronavirus. If you would like to support our journalists you can subscribe here.
Sign up for our newsletter to stay up to date.