"RPE is focusing mainly on Auckland and on its training role, and over the last 10 years I've developed into a national advocate, I guess, and I probably don't fit back into an agency manager role," she said.
"So I thought it would be best if I moved on and created a space so they had someone who was fresh and could focus on Auckland and training and education in high schools."
She will leave the agency on May 1 and will take a four-month "sabbatical" to visit her father, who is turning 80, in Britain. She will then look for a new role in the sector back in New Zealand.
Debbi Tohill, a former manager of Auckland University's Werry Centre, has stepped down from her role chairing the RPE board to replace Dr McGregor as acting director for six months.
New co-chairman Paul Prestidge, an Auckland Council community development worker, said the board wanted to review the role before seeking a permanent replacement.
"Rather than just finding another Kim, let's have a closer look at what our best areas to work are," he said.
He and fellow co-chair Debbie Wiesehan, who manages the Life Centre Church's Streetreach agency for prostitutes, said the board supported Dr McGregor and "wish Kim all the best in her new endeavours".
The other board members are public health consultant Maggie McGregor, Auckland University psychologist Dr Gwen Willis and radio host and drug and alcohol worker Richie Hardcore.
Tania Blomfield, who replaced Dr McGregor as co-chair of Te Ohaakii a Hine-National Network Ending Sexual Violence Together, said she was sad that Dr McGregor was leaving RPE but glad that she would be "jumping right back in there with both boots" after her "sabbatical".
Last year's Budget gave $10.4 million for sexual violence services for two years while longer-term funding is considered. The Social Development Ministry recently called for applications to fill gaps in areas where there are no specialist services.
Last month, the Accident Compensation Corporation restored a fully funded counselling service for sexual violence survivors.
"I just can't sing ACC's praises highly enough," Ms Blomfield said.
But she said the national network's funding had not yet been extended beyond this June and no one yet knew what would happen when the sector's two-year funding ended.
"So the financial situation hasn't really changed," she said. "Everyone is still anxious."
Dr Kim McGregor
•Therapist with survivors of sexual violence since 1986.
•Wrote two books of survivors' stories: Warriors of Truth (1994) and Surviving and Moving On (2008).
•Director of Auckland Rape Crisis/Rape Prevention Education since 2005.
•Co-founded national network on ending sexual violence in 2005 and chaired it 2009-13.
•Member of Taskforce for Action on Sexual Violence 2007-09.