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Brash has accused Clarke of getting involved in New Zealand race relations and meddling in the "politicised" 250-year anniversary commemorations of Cook's arrival, calling for her to be withdrawn from her post.
"She acknowledged Cook's regret over the deaths but inflated the death toll to nine without acknowledging that he recorded in his diary four or five deaths at Gisborne," he said.
"Unwittingly, the British High Commissioner sided with activists and helped them score a major propaganda point."
Dame Anne Salmond, a prominent historian from Gisborne who has been part of conversations about the deaths with Tūranga iwi, said the truth was there was uncertainty about what had happened and that direct witnesses to the events had disagreed.
She said it was generally agreed nine people had been shot, at least four or five fatally, but it was not clear how many of the others were killed.
"Trying to make this a simple matter is extremely unhelpful, which is what Don Brash is trying to do … because the fact of the matter is the accounts themselves are confused about how many people died," she said.
"When you're shooting people with muskets you can't necessarily see who's dead and who's not."
She said Tūranga historians had been incredibly careful in their accounts.
"My experience of working with tribal historians on this is that they know the information extremely well."
The High Commission declined to comment on Thursday and requests for comment from iwi have not been returned.
The Tuia250 events marking 250 years since Cook's arrival have been dogged by controversy.
The iwi that hosted the British Government has refused to take part in a welcome for a replica of Cook's Endeavour which is due to visit Gisborne next week as part of a flotilla of tall ships and waka.
The northern iwi of Ngāti Kahu also opposed the Endeavour docking at Mangonui in the Far North.
Brash said the events had become "politicised with racist allegations against Cook" and the British Government needed to butt out.
A former leader of the National and Act parties and a former Reserve Bank Governor, Brash now leads the Hobson's Pledge group, which campaigns against favouritism under the Treaty of Waitangi.
Prime Minister Jacinda Ardern did not attend the ceremony and on Thursday continued to maintain distance from the event, saying it was for iwi to decide whether she was there. She was not asked about the Brash claims.
"My very strong view was that it was a matter for local iwi and I was absolutely prepared to follow whatever their expectation was," she said.
"This was not a matter for the New Zealand Government."
Ardern will be present for several days at Tuia in Gisborne from this weekend, and said it was a chance for significant conversations about New Zealand's history.