The top half of North Island was struck by severe thunderstorms on Tuesday, leading to flash flooding and the declaration of a local emergency in Auckland.

In Whangarei, emergency services were called at 10.35am to Abbey Caves, where a group from Whangarei Boys High School were in difficulty.

Local media reports a group, including two supervisors and at least a dozen year 11 students, were trapped in a cave.

Northland District Commander Tony Hill said rescue teams attended the incident, with all but one of the students making it to safety.

"The incident is still very much developing and we will provide further updates as they become available," he said.

"Our thoughts are with the whanau of the missing child, as well as all those involved in the group outing and the school."

Abbey Caves is a series of limestone outcrops, sinkholes and caves in hills nearby Whangarei which are prone to flash flooding.

"Only experienced cavers should enter the underground caves, as there are risks from rapidly rising water and roof falls," the council's website states.

Whangarei received 60 millimetres of rain in the three hours to midday in the big wet.

It is not yet clear whether the group were aware of the looming storms when they committed to the trip.

School board chairman Andrew Carvell told news outlet Stuff it was a "very traumatic situation" but he remained hopeful of a positive outcome.

"We anticipate there are going to be questions. ... Those questions are reasonable questions to ask," he said.

Speaking at parliament in Wellington, Prime Minister Chris Hipkins gave his "deep concern" for the missing teenager.

Later on Tuesday afternoon, MetService issued a rare red warning - saved for the most destructive weather events - due to the severe storms passing through the region.

Aucklanders have shared photos and video of rising floodwaters waters swallowing up fields and taking over roads on social media.

The transport agency reported significant delays on motorways due to flooding and accidents across the region.

Many ferry and train services were suspended and motorists have been urged to delay any non-essential travel.

"It is a serious situation in Auckland," Mr Hipkins said.

"Right now, my request to people is just keep yourself safe, keep yourself physically safe. We will support you through."

The rain is a reminder for Aucklanders of major flooding in January, when four men were killed in a monster rain event which caused an estimated billion dollars worth of damage.

Auckland Mayor Wayne Brown, currently in Sydney, made an emergency declaration just after 1pm on Tuesday.

He was widely criticised for delaying a similar call during January's floods.

The front is expected to lash northern North Island until Tuesday evening, before easing.

Australian Associated Press