Whitelock, Richie Mo'unga and Aaron Smith did not travel to Australia with the rest of the All Blacks squad earlier this month as they remained in New Zealand on paternity leave.

The final matches in four-nation competition are being played in Queensland from Sunday until October 2, but the 32-year-old Whitelock was unable to secure a place in quarantine in Australia early enough to be available.

"Samuel Whitelock is to stay in New Zealand and will miss the rest of the Rugby Championship," New Zealand Rugby said in a statement.

"The timing of arrival meant that Whitelock would have exited his two weeks' hard quarantine with not enough time for a tight forward to safely prepare to play against South Africa on October 2.

"New Zealand Rugby understands that quarantine spots in Queensland are limited and are hugely appreciative of the efforts by Queensland Health, Rugby Australia and SANZAAR in assisting with this matter."

Lock Brodie Retallick will captain the All Blacks for the first time when they take on Argentina on Sunday at Cbus Super Stadium on the Gold Coast - in the absence of Whitelock and stand-in skipper Ardie Savea - who is unavailable due to a head knock.

Mo'unga will arrive in Queensland on Tuesday and is expected to be available for the round six clash with the world champion Springboks on the Gold Coast.

Whitelock will return to the All Blacks squad for their tour of the northern hemisphere, which begins on October 23 when they face the United States.

Australian Associated Press