Senate President Sue Lines told Thorpe, a DjabWurrung Gunnai Gunditjmara woman, that she was required to recite the affirmation - a form of the parliamentary oath that omits a reference to God - as written.
After a pause, Thorpe - a senator since September 2020 who retained her seat at a Federal election in May - recited the affirmation correctly.
Buckingham Palace spokespeople had no immediate response to a request for comment on Thorpe's remark.
Australia's Indigenous leaders have toiled for generations to win recognition for injustices suffered by their peoples since European colonisation began in the 1700s.
Prime Minister Anthony Albanese is seeking to make changes to the constitution to recognise Indigenous minorities and require governments to consult Aboriginal people on decisions that impact their lives.
On Saturday he unveiled the wording of a draft question for a referendum as part of that plan.
Reuters