Search and rescue teams found the body late on Tuesday, after responding to a distress call just before 10.30am.
A group of Whangarei Boys High School students, accompanied by two supervisors, went ahead with a caving trip despite warnings of severe thunderstorms from MetService.
Whangarei suffered flash flooding on Tuesday morning after receiving 60 millimetres of rain in the three hours to midday.
That the student went missing has caused consternation and rage in the Northland community, with many questioning why the trip went ahead.
Local media report the group of 15 year 11 students was due to go rock climbing but switched plans due to the weather.
School principal Karen Gilbert-Smith said an investigation would take place after the "hugely upsetting" event.
"In time we will seek to understand how this situation occurred, but for now I ask that we stay united as a WBHS community and provide support where required," she wrote in a Facebook post which attracted hundreds of angry responses.
Superintendent Tony Hill said police planned to abandon the search at 5pm on Tuesday, but continued into the night with the help of specialist equipment from Auckland.
"We acknowledge this event has been very distressing for the school and wider community, and that there are a number of questions the public will have," he said.
"At the moment, police's focus is on supporting those affected, and we remind people to please not make assumptions as to what has occurred."
The death comes after storms affected much of the North Island on Tuesday and Wednesday morning.
Auckland declared a state of emergency after flash flooding which brought traffic to a standstill, causing accidents.
There are about 120 properties being inspected after flood damage, with more than 300 emergency callouts.
Weather warnings were lifted for NZ's biggest city on Wednesday but remain in the Bay of Plenty and Marlborough.