Staff at the centres said they would stay open until told otherwise, as the Victorian Government continued to emphasise childcare was an "essential service".
But many local facilities have seen numbers dry up — with some reduced to 20 per cent capacity — as parents keep children at home.
Kialla Children's Centre director Nicole Short said their two kinder classes — which normally hold 21 children each — had three children in one and six in another yesterday.
“We've been instructed to remain open, but it's impacting on our staffing,” she said.
“It puts us in a difficult place, because we don't know where we stand and there's so much conflict and confusion around schools being closed but childcare staying open.
“Parents have been great, though. They've been texting us saying, ‘It's not because we don't trust you, it's just that we want to play it safe'.
“We held a morning tea for our staff this morning to keep their spirits up, as this is such an uncertain time for them with employment. But who knows what will happen next?”
While numbers are plummeting, centres are still providing a vital service to many local parents — particularly those working in healthcare, emergency services or supermarkets.
“We want to be there as long as we can to support our community and parents who are working hard to keep us safe,” Nido Early School manager Elle Trebilco said.
Centres have implemented hygiene measures to ensure the safety of children, including installing sanitising stations, regular cleaning and education for parents, children and staff.
“We want to ensure children have no risk of catching germs,” Ms Trebilco said.
“We have a checklist where we sanitise buttons, door handles, railings, iPads and more every 20 minutes.
“We are also taking kids’ temperatures each day and if children have a fever, they are asked to go home and get clearance before they come back.
“We're also using gloves and getting COVID-19 training through the Department of Health and Human Services.”
A Greater Shepparton City Council spokesperson said all council-run kindergarten, childcare centres and family day cares would continue to operate until further advice was received.
“Social distancing measures, good hygiene practices and consistent and clear messaging are just some of the measures all council services are taking to help stop the spread of COVID-19,” the spokesperson said.
“As has always been the case at council centres, the health and safety of the children is the number one priority, and every possible measure is being taken to ensure the centres are a safe place for all.
“Some families have been deciding to start their school holidays early, but council centres remain open and welcome all children.”