The Education Ministry has upset principals after it sent a letter to about 1000 schools suggesting they need special assistance.
Principals' groups say some of their members are angry the ministry thinks they need help understanding students' results and developing remedial programmes.
The Principals Federation and the Secondary Principals Association say schools with poor NCEA and national standards results were put in the lowest category, even if they have a proven track record of doing great work with children from deprived backgrounds.
Secondary Principals' Association president Tom Parsons says the Ministry focused on schools' raw results, which do not show the full picture of how well they are working with struggling learners.
"Some were a little miffed that the hard work they're doing has not been recognised and that they're being beaten up about it."
The Education Mministry has apologised to school groups for the letters, which it says were clumsy. It says it was trying to make its annual examination of school charters easier by selecting only some schools for close attention, rather than examining all 2500 schools.
The ministry says it will work with schools to find a new approach for next year.