Education Scotland's corporate plan for 2013-16 shows pupils from the most affluent areas do nearly three times as well as those from the most deprived communities.
The Education Scotland report also highlights continuing concern over the performance of some schools.
An analysis of inspection reports from 2008 to 2011 shows 36% of schools have weaknesses in the way they check their own performance - a critical way of raising standards. Around one-quarter still have weaknesses in the curriculum and in meeting the needs of learners.
The corporate plan states: "We see relatively few instances of extreme under-performance, but we see many schools and services which still have substantial scope for improvement.
"Summaries of the outcomes of our inspections over the period 2008 to 2011 show the large proportion of our evaluations fall into the satisfactory and good categories and the need to achieve a major shift towards seeing more widespread evidence of very good and excellent provision. We will not make the progress we seek simply by focusing on improving currently low-performing education providers. We need to ensure that continuous improvement is occurring broadly across the system, no matter the starting point."
Every school qualification in Scotland - from basic foundation courses to Highers and Advanced Highers - has a score associated with it.
The Education Scotland report shows pupils from the poorest backgrounds who left school in 2011/12 had an average score of some 250 points compared to nearly 600 points for those from the most affluent communities. An A grade at Higher is worth 72 points.
Iain Ellis, chairman of the National Parent Forum of Scotland, welcomed the report and called for an expansion of the number of dedicated school staff whose job it is to engage and support families in deprived communities.
He said: "All children are entitled to receive a top quality educational experience, with high aspirations about their abilities and their potential to achieve, regardless of their background.
"Extra work needs to be done within our education system to develop and sustain relationships with families from the early years through to the end of secondary school and beyond. Family support teachers might be one way to achieve this."
Larry Flanagan, general secretary of the Educational Institute of Scotland (EIS) teaching union, said it was shameful the country had not successfully tackled the growing social divide.
He said: "Improving the educational chances for young people who are disadvantaged must be our top priority, and so we must continue to push for a fair comprehensive education system that can provide all young people with every opportunity to maximise their educational potential.
"This is an issue that schools themselves, often under-resourced and facing daily challenges just to provide sufficient levels of resources and staffing to deliver teaching and learning.
"To truly tackle the blight of poverty across Scotland and improve the life chances of all our young people, we must continue to invest in our education system."
Craig Munro, strategic director of Education Scotland, said: "All the indicators conclude that Scotland has a good education system, but we want to make it a great one.
"One key area of focus is the link between social background and educational outcomes and this issue needs to be challenged if we are to improve."