The investigation by public spending watchdog Audit Scotland, published today, found "many initiatives to reduce health inequalities have lacked a clear focus from the outset on cost-effectiveness and outcome measures".
Some parts of the country have focused on the inequalities issue and set up projects aimed at improving the wellbeing of the poorest.
However, the watchdog says that, in other areas, tackling health inequalities was considered less of a priority because most of the NHS budget was being ploughed into hospitals, compromising funding for health improvement work.
During the past 50 years the health of the Scottish population has improved but the gulf between the life expectancy of the affluent and the poor has remained. Men living in the wealthiest communities can expect to survive 11 years longer than those living in the most deprived areas – and this figure has been the same for a decade.
The Scottish Government has long talked about the importance of addressing this situation and it is estimated to have allocated £1.8bn between 2008-09 and 2010-11 for issues relating to health inequalities.
This includes initiatives in deprived areas to improve diet and exercise levels, to reduce smoking and drug abuse, to create better transport links and employment opportunities, and to enhance the physical environment.
In 2008 the Government established eight test sites under the banner Equally Well to try new ideas.
Audit Scotland acknowledges the full impact of such investment will only be clear in the long term, but its portfolio manager, Claire Sweeney, said public-sector staff needed tangible aims and it was possible to create medium-term goals.
Ms Sweeney added: "We need more transparency about the extent to which the public sector is trying to improve this problem and what progress it is making. That is where we felt there was a real gap. We need clarity about whether it is focusing resources and effort on the areas of greatest need."
The report says it is difficult to track spending by the NHS and councils on health inequalities and adds there is no evidence the Equally Well pilots have helped to address inequalities or informed service planning elsewhere.
The authors note funding for the scheme is expected to be frozen at the current level, meaning a real-terms decrease over the next two years.
Confusion around the roles different local bodies, such as Community Planning Partnerships and Community Health Partnerships, are meant to be playing in tackling inequalities was also raised.
Audit Scotland's report concludes: "The range of performance measures and reporting arrangements relating to health inequalities makes it difficult to establish a clear picture of progress."
Former NHS Greater Glasgow and Clyde chairman Sir John Arbuthnott, who has led expert groups on health board funding and the future of social care north of the Border, said: "Audit Scotland emphasise that there should be better partnership working.
"I have been saying that for some time."
However, Sir John added that the complex combination of problems which drive the lifestyle choices of people in deprived areas cannot simply be married to targets.
Professor John Frank, the director of the Scottish Collaboration for Public Health Research and Policy at Edinburgh University, said on most measures there had been no significant improvements in health inequalities in Scotland, but he also defended the Scottish Government.
He said: "At some points Audit Scotland imply the Scottish Government is not doing a good job at keeping an eye on the problem. Actually, the reports on health inequalities are the best ones in any country in the world that I have been able to find. Their eye is firmly on the ball. The ball is not moving very well."
The Scottish Government said it had shifted the emphasis from dealing with the consequences of health inequalities to tackling the underlying causes, such as poverty.
A spokesman said: "The Scottish Government is committed to reducing the health gap between the richest and poorest people in Scotland, and that is why we have recently reconvened the Ministerial Taskforce on Health Inequalities.
"The Task Force will consider the findings of the Audit Scotland Report as part of its review."