"No hurt was intended but we realise we got it wrong and apologise."
The chain's Facebook page was hammered by customers and members of the gay, lesbian, bisexual and transgender community, with many seeing the message as "disrespectful, ignorant and completely inappropriate".
Tamsyn Clemerson first posted the image of the misfortune cookie message on Friday.
"Rick rolls? Fine. Ragging on politicians and other public figures? Fine. But demeaning an extremely vulnerable sector of our population? That's pretty shit, Hells, and I'm really disappointed to find that your company is promoting bigotry under an oh-so-thin veneer of 'humour'."
Sarah Murphy agreed.
"I am really disgusted that in 2011 a large company such as yours feels that it is ok to be transphobic. You are not only enforcing hate but are saying that it is ok for others to do so too."
LaQuisha Redfern was also unimpressed Hell had mocked a vulnerable group in New Zealand society.
"Another way to look at this is to swap 'gender' for 'race'. Imagine the outrage if the cookie had said 'you will marry a darkie'. For some reason, while we find it unpalatable to be racist, many view transphobia as acceptable."
Many hoped the pizza chain would make a donation to a support group for transgendered New Zealanders.