A lack of information has made it unclear whether NHS productivity has been boosted by medical staff pay deals, Scotland's Auditor General said.
Costs and quality of treatment remain unclear, Mr Black said
Robert Black said the NHS was providing improved healthcare and "significantly" reducing treatment waiting times.
However, in his NHS performance report for 2004-05, he noted some boards had not supplied information on sickness absence and the use of agency nurses.
Mr Black called for improved workforce planning and financial management.
In 2004-05, the NHS consumed about one third, or £8bn, of the Scottish Parliament's entire budget for devolved services.
Mr Black told Holyrood's all-party audit committee that NHS Scotland spending would reach £10.3bn in two years time.
With a workforce of 150,000 the health service is Scotland's biggest employer.
However, Mr Black said sickness absence in NHS Scotland was higher than many other parts of the public sector, with 5.3% of available hours lost.
He pointed out that some health boards were failing to provide a full picture on sickness absence.
Basic information was also found to be lacking in some other workforce areas, such as the use of bank and agency nurses and progress against recruitment targets was mixed.
Mr Black said better information was urgently needed about the level and type of work being carried out in the NHS so that, for instance, the shift from inpatient to outpatient could be measured.
"There have been some improvements in the collection of activity data, such as nurse-led clinics," he said.
"But the NHS has still some way to go to provide a comprehensive picture of its activity, costs and quality of treatment."
He said there was insufficient information to explain the continuing decline in the number of planned hospital treatments for more than a decade and a levelling off of day cases and emergency admissions since 2002-03.
"It's entirely reasonable to ask the question of the health service what is happening in the system when we see that trend emerging at the same time as there are extra resources going into pay deals to improve the flexibility and quality of care," he said.
However, he added: "We do not have an explanation for this. For example, we cannot say whether the trend is a result of quality improvements or a more complex mix of cases.
"Nor can we say whether there are growing problems of efficiency.
"So the question of whether productivity as a whole is improving must remain unanswered, at the same time as we know that costs are increasing as a result of new pay deals."
The additional costs of implementing new pay deals are estimated to be £291m in the current financial year 2005-06.