Because more of the 43 boys' schools drew students with wealthier backgrounds than the 225 co-ed schools, a comparison according to decile level was also carried out.
It found that across decile groupings the percentage of all school leavers who achieved at least NCEA Level 2 was 7 to 12 per cent higher at the single-sex schools.
Maori and Pasifika school leavers from boys' schools were more likely than their counterparts in co-ed schools to gain qualifications.
NZCER chief researcher Cathy Wylie said some of the boys' schools were achieving fantastic results for their students. However, she cautioned against parents taking the results as evidence that single-sex schools were better.
Other factors at play included school size, and boys' schools including more integrated schools, which could attract parents more ready to provide financial and other support.
Dale Burden, headmaster of co-ed Mt Albert Grammar School said their boys' high performance showed the issue was not about gender intake.
However, Tony Sissons, headmaster of Remuera's private King's School, said boys' schools had benefits. "They are happy with the absence of girls, they are not competing against girls. Boys will tend not to ask questions in front of the girls."
Single-sex or co-educational?
• New research finds students who attend state boys' secondary schools are more likely to leave with qualifications than their male counterparts at co-educational schools.
• Researchers have identified what the top-performing boys' schools are doing well.
• They say what is going on inside a school should be of more concern to parents than whether it is single-sex or co-educational.
Knowing what makes boys tick
Growing up one of two sisters and attending a co-educational school in Australia's Northern Territory, Dianna Perron had never stepped inside a boys' school.
But she is now a fan of the concept after seeing sons Finn and Callum, aged 8 and 10, enjoying their time at King's School, a private primary school in Remuera.
The school understood what made boys tick, Ms Perron said.
"My boys are enormous, so they do this 'brain food' at different times during the day, knowing that boys constantly eat and are growing."
While yesterday's report looked mainly at state secondary boys' schools, it has re-ignited the debate about the general merits of single-sex and co-ed schools.
Those who prefer co-ed schools often cite the benefits of socialisation with both sexes.
Ms Perron, whose husband attended a boys' school in Palmerston North, said her sons had female friends, and she didn't think they suffered from not having that interaction at school.
