Finance director Tony Rogers was appointed as interim chief executive this week, after Ainger told CAF chair Simon Cairns of his resignation at the charity's AGM last Thursday.
Six CAF directors have left in the past year (Third Sector, 30 August and 20 September). Most recently, Tracey Reddings announced that she would leave her post as executive director of charity financial services in December to become director of charities at Barings Asset Management.
Research director Cathy Pharoah, policy director Simon Hebditch, donor services director Jenny Byers, business services director Alan Jeffs and philanthropy services director Sharon Stearnes have also departed. CAF is still advertising for a replacement for Pharoah.
One source told Third Sector: "Any organisation that loses that number of senior staff is in dire trouble. No organisation can stand that level of chaos."
Another said: "Change at CAF has been a painful process and it is ongoing - there is a lot to do and it will take a while to settle down."
Cairns paid tribute to Ainger's contribution to the charity. "Stephen has led the organisation through a period of unprecedented change and, more recently, completed the first phase of a strategic review," he said.
In a memo to staff, he wrote: "While I am aware that there have been significant changes in senior personnel, I am confident that Stephen has now put in place an outstanding senior team and that CAF has excellent staff throughout."
Ainger, a former Transco and BP executive, said: "After four years and before the strategic review moves to the next stage, I felt it was an appropriate time to move on."
Another source said: "There was a clash of outlooks. It raises the question whether people in business can really understand and work in this sector."