The centres in Adelaide's north, operated by Edge Early Learning, catered to about 50 children in Munno Para West and close to 80 kids in Gawler East.
Multiple breaches were detected by the Education Standards Board, resulting in a period of forced closure until the issues were rectified, the regulator revealed on Tuesday.
In response, the company will close all its South Australian centres on May 1 to provide additional training to staff.
The Munno Para West centre was forced to close for 90 days due to supervision and staffing issues, while Gawler East will remain shut for two weeks for failing to conduct real‑time oversight of allergen‑sensitive meal provision.
In order to reopen, the centres must comply with imposed conditions including improved educator-to-child ratios and re-training in food safety.
Parents with children at the centres were notified of the actions and provided information on alternative services through a government website.
South Australian Education Minister Lucy Hood acknowledged the closure would be inconvenient for parents, but said the safety of children was paramount.
"We do not apologise for putting the safety of our children absolutely front and centre," she told reporters on Tuesday.
"Edge Early Learning is on notice."
The company's chief executive Chris Chambers said his staff were working to minimise disruptions by securing alternative care arrangements at its nearby centres.
"These temporary closures follow separate, centre-specific matters relating to supervision and food safety documentation requirements," he said.
"In both cases, no child was harmed."
The standards board's chief executive Benn Gramola said it had been working with Edge Early Learning for some time to improve its quality and safety standards and comply with national law, but the issues had not been resolved.
"Where we see immediate risk we would close this service straight away, which is what we've done now," he said.
Mr Gramola acknowledged self-reporting by the company played a part in the breaches being identified, along with visits by the regulator.
A spokesperson for Edge Early Learning said over the past year the company had been focusing on improving a range of areas, including increasing compliance oversight and making it easier for team members and families to raise concerns.
"In practical terms, that means concerns are more likely to be identified early, escalated appropriately and acted on quickly," they said.
"We believe greater transparency and earlier reporting are signs of a system improving."
The South Australian government has pumped $29 million into the Education Standards Board and doubled its staff, leading to more unannounced visits, compliance action and service assessments.
