The Auckland District Health Board is disestablishing 20 positions in order to create new roles in areas with the greatest need.
Twenty resident doctor positions, in areas including psychiatry and obstetrics, are to go, with 20 new positions being created.
The Resident Doctors Association says the board is dis-establishing a number of critical positions.
DHB deputy chief executive Margaret Wilsher says there's not enough money to put in new positions without cutting others, but the outcome will be better for all.
She says, for example, there's a need to build a stronger geriatric team at Counties Manukau and more sub-specialist positions that are popular and will help them retain doctors.
The union says the new positions would have been created anyway.
General secretary Deborah Powell says some of the jobs the board intends to cut are "'shortage" speciailties, including six jobs in obstetrics and gynaecology and five in psychiatry.
Ms Wilsher says these roles are difficult to fill and there is much demand for the new roles.
Dr Powell says it's sad the board has no thought as to how to resolve workforce problems permanently.