Dr Pauline Kingi has stepped down from her role as head of inquiry into the appointment of Police Commissioner Wally Haumaha.
On Tuesday it emerged she had 'endorsed' Mr Haumaha 23 times on networking site LinkedIn.
Minister of Internal Affairs Tracey Martin announced her resignation in the House on Wednesday.
"Ever since she was appointed to the role, she has been the subject of political attack," Ms Martin said.
"Those have been attacks on her integrity, attacks on her reputation and even attacks on her legal qualification… She was asked to perform a public duty and yet became the subject of an undue and unwarranted criticism."
In a statement, Dr Kingi said she had an "extensive and lengthy career across public service and local government" that she is "extremely proud of".
National's Police spokesperson Chris Bishop asked Ms Martin to assure the House "that the Government will run a credible and independent inquiry that is not run by someone who has endorsed the subject of the inquiry 23 times on LinkedIn".
The inquiry will look into the process around Mr Haumaha's appointment, after comments he made about Louse Nicholas emerged.
He told Operation Austin in 2004 Ms Nicholas' claims police officers raped her were "nonsense", saying "we [officers] have to stick together."
In June, Mr Haumaha said he takes responsibility for the comments and unreservedly apologises.
He said in in the 14 years since the comments were made he has "reflected deeply and often on what it means to live the values that New Zealanders rightly expect from their police."
Dr Kingi said: "The development of the Māori Potential Framework, through Te Puni Kōkiri (TPK), the Government's primary advisor on Māori development, is something that I am extremely passionate about."
She acted as a representative for TPK on the Auckland Taumata and Counties-Manukau Taumata of the New Zealand Police, monitoring its Treaty compliance and development of its response to the Māori Potential Framework.
"I am very proud of the work undertaken to encourage one of the largest government agencies to have a positive Māori responsiveness. The culture of change that has occurred in the New Zealand Police force is something I am particularly proud of."