"There's no way it would be ... a normal response to stand a 5-year-old down," said president Paul Drummond.
"Most schools would go to almost every other option before standing down or suspending any children in primary school - it's the absolute last resort but that tells you if a child that young has been stood down, then the reasons are serious and complex and they are often to do with that child's own safety and the safety of other children."
Of the 1874 primary school cases in the year to November, 1602 children were stood down for up to five days before being allowed to return.
A further 197 were suspended, usually indicating more serious behaviour, until they could go before the board of trustees. Of those students, the behaviour of 75 was so bad that they were formally excluded from the school - meaning they had to re-enroll at another school.
While the figures provided for last year were incomplete, the numbers were on a par with 10 years ago. In 2001, 1963 primary-aged students faced serious disciplinary action.
Mr Drummond said anecdotal evidence suggested the number of children with "pretty complex behavioural and social needs" was increasing and "alarmingly, some of those children are getting younger".
Many came from dysfunctional families and demonstrated learned behaviour that schools struggled to cope with until they had extra resources or multi-agency support.
"It is not unheard of for children as young as 5 to be violent or have behaviour that you would not associate with young children," he said. "Not only are there the physical behaviours, there's the verbal behaviours and even sexual behaviours that are being presented in primary schools that perhaps you would not have associated with the times when you and I went to primary school."
Education Minister Hekia Parata said the number of incidents of "challenging behaviour in schools" had been consistent for many years.
"This level and proportion is not unusual at all, it is consistent. What is, I suppose, remarkably new is what we are doing about it because we know this kind of behaviour really can disrupt [learning]."
She said the Positive Behaviour for Learning Action plan was introduced in 2010 to help manage disruptive behaviour in schools.