Moore, who has been under pressure since the release earlier this week of a review into the culture of the team, steps down with immediate effect.
The former Highlanders and North Otago coach said it had been "an extremely difficult and emotional decision" to leave his post just six months before the Women's Rugby World Cup.
"The Black Ferns is a team of talented, motivated players, coaches and management and I unreservedly share their goal to win this pinnacle event," Moore said in a statement.
"However, I remain concerned that the prolonged Cultural & Environmental Review continues to be distracting at a time when all focus needs to be on maximising performance.
"As such, I feel it is in the best interests of the team that I step down."
The review highlighted some issues in the New Zealand high-performance women's rugby environment.
It claimed management structures did not always appropriately support the Black Ferns' culture and environment, and the culture of the team was not fully aligned with management.
The review reported some players in the team had experienced favouritism or "ghosting" from members of management, an accusation Moore addressed in his resignation statement.
"As head coach, my priority has always been to ensure that the Black Ferns team excels both on and off the field.
"However, with a large squad of committed rugby players who have all worked hard to secure a black jersey, my role involved making some tough decisions on the selection of the team.
"These decisions are always made in consultation with the wider coaching team and are never taken lightly.
"When the team is not performing at the level required for international competition, difficult and direct conversations need to happen.
"It is also important to explore different combinations in the lead up to pinnacle events. In my experience, players take the news that they are not performing, or not selected in the starting line-up, differently."
Moore acknowledged the review made it clear New Zealand Rugby needed to put training and support in place for both management and players to provide and receive feedback.
He also addressed the issue that prompted the review, the social media post by Te Kura Ngata-Aerengamate alleging behaviour that contributed to her mental health issues during the northern tour.
He said her allegations were "misleading".
"The post provided no context and unfairly and inaccurately represented me as a coach and a person.
"My values and beliefs were called into question, and it was very disappointing not only to me but also to my family.
"I have refrained from making any public comment about that until now out of concern for Te Kura's wellbeing at the time she made her post and to allow the review process to be completed.
"NZ Rugby were fully aware of my position throughout, and this was reflected in their endorsement of me as head coach."
Moore said he was grateful for the support he had received from current and former players.
It had been an honour to coach the Black Ferns for six and a-half years.
"I am proud of all the team’s achievements throughout that period, including winning the Women's Rugby World Cup in 2017 and being the first women’s team to be named World Rugby team of the year.
"These accomplishments were only made possible through the hard work and commitment of a group of dedicated players, coaches, and management.
"I wish the team the best of luck as they compete against the world’s best female rugby players at the 2022 Women's Rugby World Cup.
"You have my absolute support but now as a fan, I will be cheering for you throughout."
New Zealand Rugby chief executive Mark Robinson paid tribute to the outgoing coach.
"We understand and respect Glenn’s decision to step down and it is a mark of his character that he has chosen to put the team first at this difficult time," Robinson said.
"Glenn has been a respected and successful coach for a number of senior teams in New Zealand rugby over 20 years.
"He has been heavily involved in the transition of women’s rugby in New Zealand from a club and community level game to semi-professional and leaves with our best wishes and thanks.
"We are committed to optimising our systems and processes for our women’s game overall and to ensure the best possible outcome at the World Cup. These are key priorities for New Zealand Rugby."
A further update on the Black Ferns coaching structure would be provided next week, Robinson said.
