The boy, who is believed to be 15, was found by searchers in Abbey Caves, Whangārei.
The search was expected to conclude around 5pm yesterday, however, specialist equipment that was brought up from Auckland allowed the search to continue for longer.
This helped enable searchers to locate a body, which was successfully recovered late yesterday evening.
Superintendent Tony Hill, Northland district commander confirmed the news on Wednesday morning.
Hill said that while formal identification was yet to take place, police have ensured the family was being offered support, and their thoughts remained with them at this tragic time.
“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,” Hill 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.”
Cordons will remain in place around Abbey Caves as police conduct a routine scene examination.
According to a Stuff reporter at the scene on Wednesday morning, police were briefly at the site again but had gone by about 8.30am.
A few people who have family members at the school are at the site, holding a vigil until they find out what happened, along with Te Tai Tokerau MP Kelvin Davis.
Mata Harris said she was waiting to hear the name of the boy.
She asked why the trip went ahead when there was a weather warning.
“I think Whangārei Boys’ High School need to do some explaining,” Harris said.
“Everyone is asking the same question, why did the kids go out’,” she said.
Speaking on Tuesday afternoon, Hill said the incident was “tragic”.
“Our thoughts are with the friends and family of the unaccounted for student and Family Liaison Officers and Victim Support have measures in place to look after them.
“The school is also being supported by the Ministry of Education’s Traumatic Incident Team,” Hill said.
On Wednesday morning, the Ministry of Education confirmed this, and said they would be “supporting the school’s leadership team and will be available for as long as needed”.
“Our role is to support the school, and we will do whatever we can. Any investigation will be carried out by the appropriate agency or agencies,” the Ministry of Education’s Isabel Evans said.
Green Party MP Marama Davidson wrote on her Facebook page that she was “heartbroken” about the incident.
“I was holding deep hope that this whānau would have their tamaiti home,” Davidson wrote.
“I know we’ll all be sending love to this whānau and community. My boys are the same age as this student and I’m so deeply heartbroken for them all.”
Police first received a call about a group of 15 students from Whangārei Boys’ High School “in difficulty” in the cave at 10.26am on Tuesday.
On Tuesday, Stuff revealed that the group caught up in the floodwaters were meant to be rock climbing, but bad weather had forced the trip underground instead.
In an email sent to parents last Friday, the school’s head of outdoor education Stevie Huurnink said that due to “forecasted rain” they had to modify “planned trips”.
“Initially, we had rock climbing scheduled. This has been changed to caving,” the email said.
Parents were left wondering on Tuesday afternoon though, with one mother of a boy who saw his classmate swept away saying she had to wait hours to find out if her son was alive.
Whangārei Boys’ High School principal Karen Gilbert-Smith said on social media on Tuesday afternoon that the event had been “hugely upsetting” for the school.
The group who came out of the cave were being supported by emergency workers from Search and Rescue and St John Ambulance, Gilbert-Smith said.