Six regions also saw achievement fall in reading. There were improvements in maths across the country.
Ms Parata told the Herald she was confident those regions that had slipped would rebound.
The data comparing 2011 to 2013 gave a better indication of trend, and that was that improvements were being made.
"That tells a story over three years rather than just one year. In one year, yes, there were declines for some areas. But overall the picture is one of three-quarters of kids being at or above national standards.
"There will be specific challenges within different year levels, within genders and within ethnicities that schools will need to pay attention to. But for the purposes of telling an overall education story, this is what it looks like over the past three years."
Asked about the Government's target to have 85 per cent of children achieving the standards by 2017, she said that was a "stretch target".
National standards describe what students should be able to do in reading, writing and mathematics as they progress through levels 1 to 8, the primary and intermediate years.
The student achievement data is fiercely opposed by education unions and there have been concerns about how teacher assessments can vary between schools.
However, the Government argues it provides valuable information to parents and shows where extra resources are needed.
Yesterday, NZEI Primary President Judith Nowotarski said the new results were as unreliable and meaningless as the previous data.
"What the results show is what they have always shown - the strong link between socio-economic background and student achievement."
Ms Nowotarski said the union was concerned with how the data may be used in future, including the possibility it could be used to fund schools or teachers.
Yesterday's figures also showed improvements in school leavers' qualifications stalled last year.
The number of school leavers with at least NCEA level 2 fell 0.1 per cent to 74.2 per cent, while 49 per cent achieved level 3 (up 0.3 per cent).
The proportion of 18-year-olds with NCEA level 2 or equivalent - including those on non-school courses - was 78.6 per cent (up 1.4 per cent).
For more information visit www.educationcounts.govt.nz.