Search and rescue teams found the body late on Tuesday night, after responding to a distress call about 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.

The student's plight has caused consternation and rage in the Northland community, with many questioning why the trip went ahead.

Local media reports 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.

The student's aunt thanked emergency services on Facebook.

"We cannot express how grateful we are to all those who were involved in helping us find and bring our baby boy back to us," Kim Cuddy wrote.

A Givealittle page has been set up to support the family, with more than $NZ8000 pledged in the first two hours.

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 in Auckland, with more than 300 emergency callouts.

The storms created a tornado before dawn on Wednesday near the South Taranaki town of Awatuna, ripping roofs off two homes, according to Radio NZ.

Weather warnings have been lifted for the whole of NZ, with the exception of snow forecasts for South Island.

Australian Associated Press