Deputy public health officer Mick Cusack said the masks were first distributed among Adelaide's metropolitan hospitals on Saturday but have now been withdrawn.
"Taking extreme caution in terms of the welfare of our staff, we have removed these masks from all of the hospitals in the state, pending further advice and clarification from the commonwealth," Dr Cusack said.
"These clearly are masks that are in use across the nation."
Dr Cusack said South Australia still had sufficient protective equipment and would be in a position to produce its own in coming weeks with the establishment of a local manufacturing facility.
He said an intensive care nurse at the Royal Adelaide Hospital, who recently tested positive to COVID-19 was wearing a mask but not one of the suspect batch.
However, 34 of her close contacts are now in isolation, including 29 fellow nurses, three doctors and one ward clerk.
Concerns over the masks came as SA confirmed just one new virus case on Thursday, taking the state's total to 434.
Ten people remain in hospital with two in intensive care. One of those is listed as critical.
SA Health said 308 people had now recovered from their infections or about 70 per cent of all cases.
South Australia has also embarked on a two-week testing blitz inviting anyone with even mild respiratory systems to present at a clinic to be checked.
Dr Cusack said clinics were already experiencing increased traffic which could help unearth any undetected cases in the community.
"We don't want to rest on our laurels in terms of having low case numbers," he said.
"We're really keen to root out any evidence of infection in this state."
SA Pathology has so far tested more than 38,000 people, and given its strong performance during the pandemic, Premier Steven Marshall essentially ruled out any moves to privatise its operations.
A sale had been under consideration by the state government to cut costs but Mr Marshall said it had "fully delivered" on a new business strategy.
"I don't think we'll be privatising SA Pathology anytime soon," he said.
"In fact, I think they've done an extraordinary job."
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