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Last night Farmers was investigating the claims and said a senior executive was at the Botany store speaking to staff.
Managing director and chief executive Rod McDermott said the company teaches staff that all customers are to be treated with respect.
He said Farmers "take very seriously any claim that this has happened".
Farmers corporate relations manager Nikki Newton-Cross said the company was very supportive of the transgender community and apologised for the treatment of Mrs Haddock-Staniland and her friend.
Human Rights Commissioner Richard Tankersley praised Mrs Haddock-Staniland for going public.
He said what happened to her was not new, but rather highlighted the "bullying and hate" that transgender New Zealanders faced often.
Claudia McKay, former president of transgender organisation Agender, was surprised and disappointed at the incident and said a responsible shop assistant should not have acted in that way.
Senior law lecturer at Victoria University Catherine Iorns said from the description of what happened, it was unclear if the incident was illegal discrimination under the Human Rights Act.
"She was treated that way because she appeared a certain way, no matter whether she was physically male or female."
Ms Iorns said New Zealand's law could be seen as a bit out-of-date in that respect.
"We have updated it to take account of sexual orientation but transgender people have not yet been covered for this kind of discrimination.
"So it comes back to a standard of common decency and sensitivity in how you treat people and this is where education is needed, such as of shop assistants, so they know how to handle such situations.
"This was clearly not some prank where we had a male dressing as a female trying to sneak into a female dressing room. This was a matter of Mary's genuine identity as a female."
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