Education Ministry changes to National Standards data will result in discrepancies between this year's data and next year's, leading to fears parents will think their children are underperforming.
The ministry has scaled down term one results obtained through schools' online writing assessment tool, e-asTTLE, which means next year's results will be lower than this year's.
The latest results are set to be published next week on the ministry's Education Counts website.
Schools say they fear parents will interpret the results as their children underperforming in National Standards.
An advisory to schools was published on the ministry's website on April 30 which explained how results had been scaled and included a conversion table.
But Rae Stafford, principal of Opoutere School near Whangamata, 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. Parents will justifiably be upset about this."
Changes were made to e-asTTLE last year after it was found to be inflating children's results, Ms Stafford said.
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."
NZEI past president Ian Leckie said ministry had directly intervened in the data and schools were left confused.
The actions were further rocking confidence in National Standards, he said.
Professor of Education at the University of Waikato Martin Thrupp, who is leading a three-year study on six schools, said the standards were not national 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, he said.
"Problems with formal assessment tools are just one of many things which make national standards judgements 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 judgements in relation to National Standards, she said.
Last year Prime Minister John Key cautioned media against forming league tables, saying the data was "ropey at best".