Thomas said fans who had brought tickets in this way and had concerns should reach out to them at Ticketqueries@nzrugby.co.nz.
"If our fans have brought through our legitimate channels of AllBlacks.com or Ticketek and have abided by the terms and conditions, they shouldn't be worried about the validity of their tickets."
The All Blacks game against the Springboks is already close to a sellout, and the cancelled tickets have been reissued and are being resold to the general public.
Thomas said it was a reminder people should only buy through legitimate channels so they could be secure in the knowledge their tickets would not be cancelled.
"Our message to fans is that if you choose to buy All Blacks tickets on the secondary market through online resellers like Viagogo, you run a huge risk of not entering the venue or having to pay inflated prices for tickets."
The match is the All Blacks' second of the year after they meet Argentina in Buenos Aires this Sunday morning (NZ time).
Earlier this week, Google suspended Viagogo as an advertiser after finding it breached the search engine's advertising policies.