The Nelson-Marlborough District Health Board has finished the financial year with a shortfall of $5.2 million.
The board's annual plan shows it had budgeted for a slight surplus of $100,000 , but chief executive John Peters says the extra costs of reducing waiting times for surgery had pushed costs up $2 million more than planned.
Another factor was payment of a capital charge of $6.8 million.
Mr Peters says the board has done well throughout the year in achieving national elective targets, and no one waited more than six months for a procedure or to be seen by a specialist.
DHB chair Jenny Black says the years ahead will continue to be challenging because of an ageing population and continuing financial restraints.