The Government's spending watchdog has presented a special report on the health sector to the Dáil.
The Comptroller and Auditor General found that health boards spent €115m on capital projects without authorisation from the Department.
It meant while some projects moved on more quickly, the Department was left with no option but to fund the unauthorized capital spending once started, and it affected budgets.
The report identified deficiencies in the system used to control staffing levels, and said giving health boards responsibility for staff levels in 2001 without resolving them made the problem worse.
It found that bad planning led to money being wasted when the Eastern Health Board was changed to the Eastern Regional Health Authority with three regional boards.
In one example of poor planning, it found that €3.4m was spent on fitting out a building in Bray that was vacated after just four years.