The team said on Thursday that further scans on the anterior cruciate ligament injury revealed "more extensive damage" that would require surgery, extending his period on the sidelines by six months.
The Waikato Chiefs midfielder will now miss the entirety of next year's Super Rugby season and could face a challenging time getting back into All Blacks reckoning in time for the World Cup in France.
The news will only increase the anger in New Zealand at Swain's ruck clear-out, which All Blacks fullback Beauden Barrett described as a "free shot" on a defenceless Tupaea.
Swain was shown a yellow card for clattering into Tupaea's extended leg and later cited after officials decided the incident met the red-card threshold.
The lock was suspended for six weeks but will miss only three tests after his timely inclusion in an Australia A side for a tour of Japan, leaving him free to play some part in the Wallabies' end-of-season tour of Europe.
Swain was suspended for two weeks in July after being shown a red card for headbutting England second row Jonny Hill in retaliation for having his hair pulled.