Auckland University's director of Starpath, research associate professor Anne Hynds, said preliminary findings from Qualifications Authority data from 2005-14 showed some evidence boys were gaining on girls.
There were small gains at Level 1 and 3 but a "marked difference" at Level 2, where boys had increased in the proportion of total credits by 2.4 per cent, she said.
The controversial NCEA system phased in from 2002 has been plagued by criticism, compounded by assessment problems. Critics argued the system was weighted towards girls as it focuses on ongoing assessment rather than exams.
And some critics claim there are still cases where credits are awarded after suspect assessments.
Hynds warned the data had to be treated with caution. "We really don't know about the quality of the credits and we really don't know much what this means for different groups of students."
She said Starpath, a joint university and Government project on underachievement, was examining the quality of credits and achievement of students across ethnicities, deciles and family circumstances.
A former member of a Ministry of Education advisory panel on lifting boys' achievement welcomed the new statistics but warned against complacency. Southland Boys' High School rector Ian Baldwin said although good initiatives were happening, too many boys in their mid-teens were unable to read and write. "The issue is the gap still exists," he said.
The Ministry of Education is now working to target the gender divide through a range of programmes, particularly aimed at boys' literacy.
That includes additional funding for "gender-specific problems"; new resources to get boys reading using graphic novels; and "story starter" videos with famous New Zealanders, including comedian Bret McKenzie, actor James Rolleston and former All Black John Schwalger.
The ministry has also launched a "Success for Boys" website for teachers and is working on improved achievement data collection to spot differences in gender performance.
Stoop said educationalists had grappled with closing the gender gap for years and were determined to see boys reach their full potential.
Many schools had worked hard to support boys to engage more strongly in learning and helping them to succeed. Auckland's Glendowie College principal Richard Dykes said one way of improving boys' performance lay with "academic counselling", in which individual students' strengths and weaknesses were identified to help them learn in future.
He said there was no reason boys shouldn't achieve as well as girls, regardless of whether they went to a co-ed or single-sex school.
