Four of Wales' seven health boards failed to break-even over three years, according to a written statement by the Welsh Government.
The accounts of all ten NHS organisations, which include the 7 health boards and Public Health Wales, were audited and presented to the National Assembly.
Abertawe Bro Morgannwg University Health Board and Cardiff and Vale University Health Board failed to break even in 2016-17, despite doing so in recent years.
But Betsi Cadwaladr and Hywel Dda University Health Boards have not broken even since before 2014.
Betsi Cadwaladr UHB was placed into special measures in 2015, but the Government said financial issues were not an explicit reason.
The other three boards were placed into "targeted intervention" last September.
The Welsh Government also said additional cash was being provided to all boards failing to meet their targets, to enable them to keep up with financial commitments including paying staff.
According to the report, six of the organisations did meet budget targets.