Papers released by her office under the Official Information Act show that Ms Collins nominated Mr Kee for the role as one of 13 candidates to be assessed by an independent panel within the Justice Ministry.
The panel, which was headed by Mr Rutherford, recommended that Mr Kee be interviewed as one of six on a shortlist.
Ms Collins was shown the list and cut one of the potential interviewees, understood to be a woman lawyer from Auckland.
After the remaining five candidates were interviewed by the panel, two were recommended to Ms Collins as suitable to be appointed, including Mr Kee. But the panel preferred Ms Rodgers - who is manager (policy) in the Office of the Clerk of the House of Representatives - as the top candidate to be the next director.
Ms Collins chose Mr Kee over the first-choice candidate and recommended his appointment for five years. The position pays $200,000 to $205,000 a year.
A spokeswoman for the minister said she and Mr Kee were "known to each other" because they studied law at the same time at the University of Auckland and because Ms Collins held high-profile roles at the Auckland District Law Society and New Zealand Law Society.
"This is not unusual, and does not indicate a conflict of interest," the spokeswoman said.
The panel's recommendation report said Mr Kee, a part-Chinese New Zealander, would bring diversity to the role. But attached to the report was a letter from Mr Rutherford, who said he was writing as the Chief Human Rights Commissioner and not chairman of the independent panel.
He said he shared Ms Collins' "desire to see properly qualified women better represented in the senior ranks of public service".
"I want to emphasise the importance of wherever possible appointing properly qualified women to senior public sector roles and taking a strategic approach to that, if at all possible," wrote Mr Rutherford.
"If ministers treat each of these opportunities as a one-off appointment process, rather than a strategic opportunity to improve the gender balance, I fear we may never get to where we all want to get to."
When contacted yesterday, Mr Rutherford told the Weekend Herald that Mr Kee had been an excellent appointment and had already been of great value to the office.
Asked whether she had a strategic direction for employing women in state sector roles, Ms Collins' spokeswoman said: "When making appointments Minister Collins gives full consideration to the range of attributes she believes necessary to ensure the best person for the job is appointed.
"Also, as the Minister of Ethnic Affairs, Minister Collins is very keen to make sure that people of minority ethnicities are represented."
The identity of the top candidate was redacted from the report but she was described as "someone who understands Treaty issues and human rights and is experienced in working with marginalised people", the independent panel wrote.
Mr Kee was described as having a strong background in criminal litigation involving human rights issues all the way to Court of Appeal level.
She said the factors that influenced the minister's decision to recommend Mr Kee were the panel's favourable assessment, the fact that he would bring ethnic diversity to the role.
Robert Kee
Graduated from the University of Auckland with honours in 1986 and has worked as a barrister in Auckland since 1990.
He is experienced in criminal litigation involving human rights all the way to Court of Appeal level and was recently the convener of the criminal law committee at the Auckland District Law Society.
- additional reporting: Isaac Davison and David Fisher