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Thomson was cited for "stamping or trampling" on the head of Scotland's Alasdair Strokosch, for which he was yellow carded in the All Blacks' 51-22 victory at Murrayfieldyesterday.
Australia lock Rob Simmons was also cited after the Wallabies' loss to France.
After coming on as a replacement at the Stade de France, Simmons was cited for a dangerous "tip tackle" on flanker Yannick Nyanga in the second half of the match won 33-6 by France.
Hearings for both players will be held before independent IRB-appointed Judicial Officers in London on Wednesday (local time) when both could face bans that end their involvement in their teams' European tours.
New Zealand play Italy in Rome on Saturday while Australia face England at Twickenham.