Children's marks in National Standards will be artificially lowered this year because last year's assessment was too easy.
The change has infuriated some schools, who say the Ministry of Education should have corrected the tests instead of scaling down the results and confusing children and their parents.
The principal of Opoutere School near Whangamata, Rae Stafford, said the ministry had failed to properly communicate its plans.
"We have just reported to parents at the end of last term on data collected in term one; now that data has been changed without our knowledge," she said.
"Parents will justifiably be upset about this."
Ms Stafford said that last year, changes were made to schools' online writing assessment tool, e-asTTle, after it was found to be inflating children's results.
Instead of changing the tool, the ministry had chosen to scale down the results.
"A child that had previously come out as average was coming out as above average," Ms Stafford said.
"I don't think it's right to come in and scale results down; that's not a standardised test.
"I object to the fact that they didn't come and discuss it with the schools - there was no consultation."
Ian Leckie, a past president of the NZ Educational Institute teachers' union, said the ministry had directly intervened in the data and schools were left confused. The actions were further rocking confidence in National Standards, he said.
University of Waikato education professor Martin Thrupp, who is leading a three-year study of six schools, said the standards were not national, and nor were they standard.
Results from the schools in his study showed National Standards were being affected by many sources of variation at national, regional, school and classroom level, Professor Thrupp said.
"Problems with formal assessment tools are just one of many things which make national standards judgments not comparable across schools."
A ministry spokeswoman said a review of the e-asTTle tool results by a group of curriculum experts, principals, teachers, professional development facilitators and researchers had recommended scores be realigned to "ensure greater accuracy with the curriculum level reported".
"Each student's scores for writing assessments carried out since 2012 have been updated in e-asTTle to make sure all results are comparable and to enable teachers to have the best information about student achievement in writing," she said.
The results were only one source of information teachers could use to inform their overall judgments in relation to National Standards, she said.
Last year, Prime Minister John Key cautioned the media against forming league tables, saying the data was "ropey at best".