A student, also on the water, saw the duo capsize and used an emergency hand signal to raise the alarm with the crew on Perfect Day.
Staff responded quickly and within 15 minutes had rescued the girl. The only physical marks of her ordeal were minor cuts to her hands, feet, and head.
The boy took refuge on a small ledge with his attempted rescuer, a Perfect Day staff member, while they waited for help from the Northland rescue chopper.
Pilot Gerhard Pistorius said the "complex rescue" involved winching a rescue swimmer into an inflatable dinghy to assess the situation as the distressed student couldn't be seen from the air.
Land Search and Rescue New Zealand alongside St John Mid-North Territory Manager Andrew Fergusson, a trained rescue swimmer, retrieved the boy from his two-hour stint stuck in the cave and took him to the safety of the boat.
"It was a highly technical water rescue as we were dealing with challenging environmental conditions including swells," Fergusson said. "We were well prepared and our training paid off. It was a successful rescue."
As the rescue unfolded at sea, the 4pm pick-up time passed and no children were in sight. News of the rescue spread among increasingly concerned parents who were scattered along the shore, at nearby restaurants and the Tutukaka Marina car park.
One mother, who wanted to stay anonymous, said her husband was tasked with picking up their daughter and went into the Dive Shop to find out where Perfect Day was.
Staff then informed him "a child stuck in a cave was safe and the air ambulance had dropped a medic to help get the student out".
He promptly filled in other parents, who were "distraught" to hear the reason for the delay.
She said she had concerns over the trip after being told the students were not wearing lifejackets and that the boy caught in the cave had removed the wetsuit that had been issued.
"I want to know why students weren't wearing them. Two students could have easily not come home," she said.
Dive! Tutukaka Perfect Day manager Kate Malcolm said the two students and her staff member were "bruised and shaken" and recovering at home.
Malcolm said she empathised with parents not present who heard news "that has left them wondering about their child's safety".
"They have every right to ask questions, and I am confident that my team had their safety at heart during all steps of the day."
She said her staff scoured the area for concerned parents who had not heard about the rescue to fill them in on information as it was relayed.
"At this point, the rescue operation was under way and communication was limited to the rescue helicopter and the skipper of our vessel via radio."
Malcolm said Dive! Tutukaka would review the incident itself and cooperate with external inquiries.
She said wetsuits had been issued to all students as "flotation devices" and lifejackets were available to any who wanted one. She also said they had a strict protocol for assessing capabilities in the water which were adhered to by staff on the day.
A Maritime NZ spokesperson said it would work alongside Dive! Tutukaka to investigate the circumstances around the event and what safety systems were in place.
"Under New Zealand law, commercial operators are required to have robust safety systems in place. Maritime NZ takes incidents of this sort very seriously and will be working with WorkSafe and the Northland Regional Council to establish the next steps."
Tauraroa Area School principal Grant Burns said he had "full confidence" in Dive! Tutukaka which had hosted school trips for more than 10 years without incident.
"We are really pleased that the incident had a happy ending. We are hoping this incident doesn't ruin education outside of the classroom - it's such an important aspect of learning."