Public spending watchdog Audit Scotland also reported signs of growing strain on the health system, which is having to cope with tighter budgets and a growing number of elderly patients.
The watchdog's experts have called for a greater focus on financial planning for the future in their evaluation of NHS finances, although all health boards did meet their budget targets last year.
Scottish health boards spent £10.9 billion over the 12 months to April 2013, which is almost one-third of total public spending in Scotland.
Health boards ended the year with a surplus of £16.9m, but they will need to identify savings of about £268m to break even this financial year - and it is repeatedly being reported that easy targets for savings have been exhausted.
Gemma Diamond, project manager for Audit Scotland, said: "We really noticed in 2012-13 some of the pressures are starting to show, in terms of waiting times targets not being met, increased use of agency and bank staff - where there has been decreases in expenditure in previous years -and increases in vacancy rates of consultants and nurses.
"There are a range of pressures that we have seen this year that have not been present in previous years as much."