The changes have been motivated by a desire to make better use of staff and facilities across the region, and to ease financial pressure after the three DHBs set a break-even target for the 2013/14 financial year, said Mr Francis.
Hutt Valley and Wairarapa DHBs boards will remain separate to retain some local representation, although some committees will merge and planning and funding services, including that of Capital and Coast DHB, will merge to create a Service Integration Development Unit.
A gradual integration of clinical and support services would occur, although Mr Francis said most staff would not be affected immediately.
Mr Francis said there was no indication that services would be reduced, as none of the four campuses across the DHBs had any spare capacity.
The process of appointing a joint chief executive would begin immediately, and that person would decide on a new structure for the senior management team.
Mr Francis said there was still some work to do around where the positions would be based, but Wairarapa DHB's board would have some "bottom lines" around presence in Wairarapa.
Wairarapa DHB chief executive Tracey Adamson said it was inappropriate to comment on whether she would be applying for the new position, but emphasised that she was supportive of the moves and it was the best thing for Wairarapa.
"This is going to deliver better patient care, making the system work for patients and staff not making the system work just because that's what the system does," Ms Adamson said.
"We need to be brave in our decisions."
Graham Dyer is the chief executive of Hutt Valley DHB.
Ms Adamson said joint appointments across the two DHBs would allow Wairarapa to get better services, already proven by the appointment of a second speech language therapist who works in both areas.
She said there had not been a figure on the savings the partnership would create but it was "in the millions, not just a few hundred thousand".
The three DHBs have made a commitment to look at joint appointments as vacancies arise, but redundancies were possible, although other options such as relocating or retraining staff would be looked at first.
Ear, Nose and Throat, gastroentrology, child health and palliative care have already joined, and during the coming months radiology, laboratory, dermatology, elective surgery and health of older people could be affected.