A child under the age of three is one of six COVID-related deaths reported in SA on Thursday, as the state also grapples with a sharp surge in influenza cases.
SA Health said the cause of the child's death was still being determined and the case has been reported to the coroner, as per standard practice.
Chief Public Health Officer Professor Nicola Spurrier said the child was "previously well" and had "some mild respiratory symptoms".
Professor Spurrier said while the child's death was "really tragic", it was a "very rare" occurrence.
"Usually COVID in young children is very mild," she said.
Nearly 90,000 children under the age of 11 have contracted COVID since borders opened on November 23 and three children with COVID have died.
Of the 222 people currently in hospital, 10 are children under the age of nine.
"I know that parents who have heard this news will be pretty worried and will be concerned that something may happen to their young child if they catch COVID," Professor Spurrier said.
"And the best thing families can do, because we're not vaccinating that age group, is make sure everyone else in the family is vaccinated."
Professor Spurrier said all eligible South Australians should ensure they had received three doses of a COVID vaccine.
"It is a nasty virus, we shouldn't underestimate it," she said.
South Australia recorded 2,983 new COVID cases on Thursday and five other deaths were reported including a man and woman in their 90s, two men in their 80s and a man in his 70s.
Flu cases increasing
Meanwhile, more than 3,500 flu cases have been recorded in the state compared to 16 around the same time last year, chair of Immunisation Coalition Rod Pearce told ABC Radio Adelaide.
Last week alone about 1,000 flu cases were reported.
"We've got a population that hasn't seen influenza for a couple of years so it's going to hit us quicker," Dr Pearce said.
"There are children who've never seen flu because they're born after the last [flu] season."
Had the flu been circulating in the past two years, Dr Pearce said the population would have had "a natural boost" to their immunity.
SA Health data shows 238 people have been admitted to hospital because of the flu.
Most cases in South Australia are the Influenza A strain.
Two out of five South Australians are vaccinated against the flu, but Health Minister Chris Picton said that was not enough to combat the surging numbers.
"That increased number of flu cases is having an impact on hospitals that are already overwhelmed with COVID cases and other respiratory conditions," Mr Picton said.
"We do want to see more and more younger South Australians come forward and get protected for the free flu vaccine because we know that the number of cases that we're seeing in younger people are quite significant.
Meanwhile 2,983 new COVID cases have been reported on Thursday and there are 15,960 active cases in SA.
Doctors want more transparency
Queensland was the first state to announce free flu shots in May.
South Australia soon followed suit, with free flu vaccines available until June 30.
But Dr Pearce said the SA announcement threw GPs and pharmacies' planning into disarray as they reimbursed people who had paid for a vaccine.
"It's typical of what's been happening with vaccine programs — not just with flu but with COVID – that was being announced on the run," he said.
"We're not saying they are bad things but as providers, we weren't told about [the announcement of free flu shots].
Dr Pearce said the lack of transparency caused frustration for GPs and pharmacies, who learnt of changes through "a press release".
