Players and up to 100 spectators were caught up in the brawl, which erupted in the last minute of a semifinal between Auckland Grammar and Kelston Boys' High on Saturday.
The fight, after a last-minute Grammar try sealed a 20-9 victory for the school, lasted five minutes and led to at least one schoolboy being knocked out, according to a witness.
The violence was described as "extremely disappointing" by spectator and All Black coach Graham Henry, a former coach of both schools' 1st XVs.
Auckland Rugby Union chief executive Andy Dalton said the fight was "appalling" and a "bad look" for the game.
Its judiciary would now decide what penalties, if any, would be imposed, he said.
It was likely both teams would appear before the judiciary this week.
The union would also speak to the headmasters of both schools and seek a full report from the referee manager, Mr Dalton said.
The two schools blamed each other for the fight.
Auckland Grammar headmaster John Morris told the New Zealand Herald newspaper a Kelston player "king hit" one of his players out of frustration after a try was scored.
But Kelston principal Steve Watt said film of the incident showed one of his players being punched twice by a Grammar student before the try was scored.
Mr Watt and Mr Morris said they would both be reviewing film of the brawl before deciding whether any disciplinary action would be taken.
Manoj Daji, chief executive of College Sport, the body in charge of high school sport, said that if the brawl was reported to him today, it would be the first complaint involving rugby this year.
He said the violence was "mainly adults behaving badly", sentiments echoed by Secondary Schools Rugby Union secretary Alex Bing.
"If people hadn't come across the field, I'm sure the whole thing would have died off within half a minute," he said.
Both Mr Morris and Mr Watt agreed the incident was a "one-off" and was not likely to happen again.
They were keen to see sporting exchanges between the schools continue.
"There is a tremendous respect and relationship between the two schools and this certainly won't sour it in any way," Mr Watt said.
