The All Blacks lock suffered a “significant injury to the structures supporting his big toe” in a training game earlier this month, the Crusaders said.
“Scott will miss the remainder of the Super Rugby Aotearoa competition to undergo surgery and allow sufficient time to recover,” a statement said, adding that his return date was uncertain.
All Blacks hooker Codie Taylor will take over as Crusaders captain, while Alex Ainley has joined the squad as injury cover.
The Crusaders are the dominant side in Super Rugby, winning the last three editions, and they beat the Wellington Hurricanes 39-25 in their Super Rugby Aotearoa debut last week.
Barrett, 26, brother of fellow All Blacks Beauden and Jordie, sat out that game with his injury.
Super Rugby Aotearoa is a temporary, New Zealand-only replacement for the wider Super Rugby competition, which is suspended because of the coronavirus.
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