Ms Houliston's resignation was announced yesterday in a brief media statement from board chairman John Walsh.
Ms Houliston had resigned "citing philosophical differences with the board on some key issues", he said.
Her resignation was effective immediately, and staff were informed yesterday, he said.
Ms Houliston, of Dunedin, could not be contacted late yesterday, and Mr Walsh would not elaborate on the circumstances when contacted.
"I won't say much more than that ... It's not an unknown phrase in these circumstances. There are differences which are of a philosophical nature, and they are about the direction [in which] the organisation should proceed.
"She has decided it would be better if she left," Mr Walsh said.
He declined to comment when asked if her departure was connected to the dismissal of five award-winning Wanaka Cancer Support Group volunteers in June last year.
The dismissal of the five - Jonette Hodge, Margaret Barrow, Barbara Bayliss, Alison Stretch and Michelle Rowe, followed by the resignation of a sixth, Julie Mulholland, in support - came after a clash with a senior staff member over the allocation of resources.
Their dismissal, under Ms Houliston's stewardship, was followed by mediation and the offer of an apology by Ms Houliston, later rejected.
Yesterday, Mr Walsh confirmed the senior staff member with whom the volunteers had clashed no longer worked for the organisation, having also resigned.
However, the resignation of the staff member - whom Mr Walsh declined to name - was "unrelated" to Ms Houliston's departure, he said.
Asked if Ms Houliston was asked to resign, Mr Walsh responded: "No comment."
Mr Walsh said the board "respects Wendy's decision", acknowledged her service and wished her well. He added she would continue to support the society's work "in a less formal capacity".
The search for a replacement would begin soon, but services to cancer patients in Otago and Southland would continue as usual, he said.
