But it says a general narrowing of the gap, across the OECD as well as in New Zealand, shows that inequality does not have to be "a fixed feature of education systems".
"All countries can reduce the impact of socio-economic status on student performance, given the right education policies and practices," it says.
It recommends scrapping ability-based "streaming", helping teachers to tailor their teaching to the needs of each student, giving more resources to schools with poorer students, and improving communication with parents in poorer families.
"Though managing classrooms with students of different levels and backgrounds may require the adoption of new tools and teaching practices, such settings prove to be the most beneficial for disadvantaged students," it says.
The gap between rich and poor students is still huge. On average, the poorest quarter of 15-year-olds scored 88 points below the richest quarter of students in the OECD Programme for International Student Assessment (Pisa) in 2015 - "equivalent to about three full years of schooling".
In New Zealand, the gap was even wider, at 101 points on a scale where the world average is fixed at 500 points.
On some measures, the socio-economic gap in New Zealand has continued to widen. For example, the proportion of poorer NZ 15-year-olds feeling that they "belong" in school slipped from 81 per cent in 2003 to 66 per cent in 2015.
Poorer 15-year-olds in New Zealand are now 13 per cent less likely to feel that they "belong" in school than richer students. This is the same gap as in Australia, but a wider gap than in 29 out of 35 OECD countries.
At their peaks between 2006 and 2012, the OECD estimates that socio-economic status explained up to 19 per cent of the total variation between NZ 15-year-olds in maths, 16 per cent of the variation in science and 17 per cent in reading.
It says socio-economic status now accounts for only 14 per cent of the NZ variation in maths and science, and 12 per cent in reading.
The averages across the OECD are now very similar: 13 per cent for maths and science and 12 per cent in reading.
The report also examines a small group of 12 countries which have measured maths achievement of a cohort of young people who were born in about 1985 and have been asked in three surveys since then about one measure of their parents' socio-economic status - how many books they had at home.
New Zealand's gap in maths achievement between those with more than or fewer than 100 books at home was the widest of any country in the 12-nation group when the students were tested at the age of 10 in 1995.
But the gaps widened by less in New Zealand as the young people grew older than in any of the other countries except South Korea. By the time they were tested again in a survey of adult skills when they were aged 25-29, the NZ gap between young people who grew up with or without books was only the fourth-widest in the group.
Ministry of Education deputy secretary Dr Craig Jones said the ministry recognised that New Zealand's education system "is not delivering equitable outcomes for all students".
"We're committed to shifting the dial to ensure all New Zealanders have access to high quality, fair and inclusive education," he said.
"Equity and wellbeing are at the heart of the education work programme, now underway, which is a major opportunity to ensure the system provides for all learners."
