The Southland and Otago District Health Boards say Government demands on budgets mean services for the disabled are being reduced.
In December last year, Health Minister Tony Ryall wrote to all boards telling them they must redouble efforts to stick to cost plans.
Southland has been told its budget deficit must fall to $5 million, while Otago is to trim its operating excess to $7 million.
The boards say their budgets are particularly challenged by increasing staff costs.
The Association of Salaried Medical Specialists says boards should be given more time to address budget blowouts and they need to stand firmer against Government pressure.