New Zealand police said on Wednesday they had recovered the body of a teen killed during a "tragic" school caving trip that is now the subject of a comprehensive investigation.

The teen was visiting the popular Abbey Caves complex north of Auckland on Tuesday when his class "encountered a severe weather event".

After a day-long search in squalid weather, police said a body was recovered late Tuesday and the boy's family was being offered support while the formal identification takes place.

"Our thoughts remain with them at this tragic time," Northland police superintendent Tony Hill said.

Well-wishers left flowers at the caves, which remained behind a police cordon Wednesday.

"I think it is every parent's worst possible nightmare to send your child off to school in the morning and not have them returned safely home in the evening," Prime Minister Chris Hipkins said, according to the NZ Herald newspaper.

Questions have been raised about why teachers took more than a dozen 15- and 16-year-olds from Whangarei Boys' High School to an area highly prone to flash floods.

The area received about 13 centimetres of rainfall (five inches) on the day of the trip and there was widespread flooding.

Principal Karen Gilbert-Smith said Wednesday the school and local community were "devastated", having lost a "much loved and treasured son and brother".

"I realise that people have lots of questions, but I simply am not in a position to provide answers at this early stage," she said.

"We need to allow a full and comprehensive investigation involving the NZ Police and Worksafe NZ into this tragic incident to be completed."

Police have refused to provide details about what they believe occurred in the caves, but warned the media "to not make assumptions".