"During consultations with the Department of Internal Affairs, it was established that the documents could be issued in the applicant's preferred sex/gender."
A letter from the UN high commissioner, lodged together with her resettlement documentations, said it, too, accepted Ms Rubashkyn as "female".
Mr Piercey said her identity had been recorded as female in the agency's application management system to reflect her new name and gender.
David Schnellenberg, spokesman for Internal Affairs, said people could choose to be registered as either male or female when applying for a passport.
"This development was achieved after a review in consultation with the Human Rights Commission and the transgender community," Mr Schnellenberg said.
Ms Rubashkyn said she had inquired about being resettled in France, Norway and Finland, but all three countries required that she undergo surgery to become a woman.
"I am afraid of surgery and I feel the gender is a cultural and social construction and it's not a biological thing," she said.
"Whether I have surgery or not should not be the business of governments, it is my own business."
Ms Rubashkyn, who arrived in New Zealand on May 30, said her fight to be classified as a woman had not been easy.
Hormonal treatment had changed her male look she was born with to become more feminine, but that resulted in confusion.
In Hong Kong last year, she was refused entry at the border because her appearance did not match the "male" identity on her Colombian passport.
Ms Rubashkyn said she had been dressing as a woman since she was 17, and had been treated "like an outcast" since.
"In Colombia, when I was 21, someone tried to rape me when I was walking down the street," she said.
"I have been through hell, and I am so appreciative and happy that I can start my life anew here in New Zealand as a woman."
Regulations
Sex change in NZ passport
• Applicants can choose preferred sex/gender identity from M (male), F (female) or X (undetermined).
• No need to amend details on birth or citizenship record.
• Must complete a statutory declaration indicating how long current sex/gender identity has been maintained.
• Under 18s require statutory declaration from a parent or legal guardian and a registered doctor or medical professional.
(source: Department of Internal Affairs)