Maori and Pasifika students continue to trail other pupils, despite Pasifika students making the most progress between years.
Male students were also lagging in reading and writing achievement compared to their female counterparts.
Individual year-level data, released for the first time since National Standards were implemented, shows standard achievement between years dropped in the maths and writing disciplines.
Mr Stanton said student progress, particularly at the intermediate level, could be overlooked in the National Standards system.
"For a student to move right through one level of the curriculum, it typically takes around 18 months." Some students made significant progress during a year "but it won't actually show up because of the sweeping nature in which National Standards are being measured".
Comparing results between schools could also be problematic, he said.
"Interschool comparison at this time is really suspect because we don't have any form of national moderation going on to ensure there is validity between schools. There is an option whether schools undertake moderation processes or not ... but it's not a requirement."
Results for Northland schools are due to be released later this month.
The country's largest teaching union, the New Zealand Educational Institute, slammed publication of the results - saying the most recent data failed to contribute anything new.
President Judith Nowotarski said the National Standards were as unreliable and invalid as last year in terms of judging teacher or school effectiveness.
Educators have warned of consistency problems in the reporting of National Standards achievement results since the system's 2010 implementation.
Education Minister Hekia Parata said the data gave a "comprehensive picture of our system and what we need to be focusing on". An expert advisory group investigating issues has been established.