Just last week, Mr Morrison told Adelaide radio Senator Antic was double-dose vaccinated.
Mr Morrison said he had been advised by Senator Antic that he was fully immunised.
The prime minister said he was “disappointed” he was misled by Senator Antic and that Mr Morrison’s radio statement wasn’t corrected by the senator.
“That was certainly my understanding that he had been double vaccinated, and I had discussed vaccinations and made it very clear that that’s what I understood,” Mr Morrison told reporters on Friday.
“I was surprised to learn that, it’s as simple as that. I was advised he was double vaccinated.”
The prime minister said Senator Antic was entitled to his choice to not get vaccinated.
“I was of the understanding that he had been double vaccinated and my office had been advised he had been double vaccinated,” he said.
“I could only work on that assumption, and that assumption proved to be incorrect.”
Asked on Friday why he was taken to a hotel to quarantine for two weeks, Senator Antic told ABC radio that was “a very good question”.
“That’s a question you might like to direct to the bureaucratic overlords at SA Health,” he added.
“I seem to have been singled out in what appears to be a political stunt and the only inference you can really draw from this is this has been quite pre-meditated,” he told the ABC.
South Australia is on high alert after discovering 18 new cases of COVID-19 in the state on Thursday.
Sixteen of the new cases are linked to one event at suburban Norwood last weekend. The other two involve travellers from interstate.
All of the infected people who attended the Norwood event, a school reunion, were fully vaccinated. Former SA premier Jay Weatherill was among them and has tested positive.
The cluster has forced 210 close contacts to quarantine for seven days but officials expect that number to increase.
Among the close contacts forced into isolation are Governor Frances Adamson, Opposition Leader Peter Malinauskas and his deputy Susan Close.
They have all tested negative, but are continuing their quarantine under the rules.
Premier Steven Marshall said the spike in virus cases was not unexpected after the state dropped most of its border restrictions last month.