Some district health boards owe staff more than a million hours in leave entitlements.
Canterbury and Waikato district health boards are both carrying more than a million hours of staff leave on their books, although the Waikato board has almost half the staff of its southern counterpart.
Waikato's chief financial officer Maureen Chrystall says managing leave is just part of the challenge of dealing with a 24/7 industry, which is often busiest when other sectors are taking holidays.
A report to the Canterbury board says the amount of leave taken in recent years has stayed the same, despite an increase in entitlements.
The report - from the general managers of hospital and specialist services - shows the total leave owing in Canterbury is 1,099,936 hours.
It says many areas are facing the challenge of balancing a high number of vacancies with managing rosters to get people to use their leave.
The report says a number of methods will be used to reduce the amount of owed leave.
These include reducing vacancies, paying out leave if more than two years of it is outstanding, and directing leave to be taken at quieter times of the year.
The union for senior doctors, the group with most leave owing, says heavy workloads are a major barrier to its members taking all the leave they are entitled to.
Executive director of the Association of Salaried Medical Specialists Ian Powell says there may be a generational factor, with some older specialists reluctant to take extended leave.
He says overall workload is also a major problem, with many specialists returning from leave to find they get hit with a large amount of work that has accumulated.
Mr Powell says the solution is to increase the number of specialists working in public hospitals.