The inequalities are "astonishingly complex" and MSPs and others must show the political will to deliver consistent and nationally scaled solutions to make a difference over the coming decade, Chief Medical Officer for Scotland Sir Harry Burns said.
Sir Harry was giving evidence to Holyrood's Public Audit Committee on a report into health inequalities by Audit Scotland. The report found that despite general improvements in health, deep-seated differences remain between the least and most deprived communities.
It found that it is not clear how, at local level, resources are targeted to the areas with the greatest need, while health spending actually tends to lead to greater benefits for richer areas.
Sir Harry said the report would have been "really helpful" 20 years ago. He said, however, it did not pay much attention to the "complex science" that underlies inequalities. "For me, health inequalities are the biggest issue facing Scotland just now, because not only are health inequalities a problem, but they are a manifestation of social inequalities and social disintegration that drives things like criminality, like poor educational attainment, and a whole range of things that we would like to be different," he said.
He said a "pan-societal" response was needed.
Conservative MSP Mary Scanlon said Audit Scotland had looked at Government strategies aimed at improving health since 2008 but the public spending watchdog had not found robust evidence of their effects.
Sir Harry said the projects are being done "piecemeal" and would have to be scaled to a much greater level. "This is not something that is going to change overnight," he said. "It will take stick-ability and doing it for five to 10 years, and then we will see a difference."