The 22-year-old has been told he will require around three more weeks of rehabilitation after picking up the problem in a match against France in November.
That raises serious question marks over his involvement in two Tests against Wales and one against Scotland, beginning on June 14.
Etzebeth was one of 10 players to play no or little part at the South Africa training camp in Durban this week, and his absence comes as a further blow after Adriaan Strauss was ruled out of the Welsh fixtures with a three-week suspension.
“Eben’s situation is a major setback as he’s been one of our best players in the last two seasons,” said coach Heyneke Meyer. “We’re continually monitoring his injury, because he really wants to play for the Springboks next month.
“However, he is still young and has a highly promising career ahead and his welfare is the most important to us.
“Player welfare is incredibly important to us. We”ve been working closely with the franchises and have taken the decision not to take any risks with players carrying injuries at this camp.
“Our medical team worked very hard at the camp, performing medical assessments on all the players and ensuring they get the best possible treatment on behalf of the franchises, as four of them are still playing Vodacom Super Rugby this weekend.
“A final decision on the involvement of all the injured players will be taken later this week, before we announce the final squad for the Castle Lager Incoming Series on Saturday.”
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