A man believed to be fugitive father Tom Phillips was shot dead by police after a confrontation early on Monday in the Waikato region, leaving one child recovered and two children still missing as officers mounted a major search operation.

Police said the suspect and a child were stopped by road spikes on a rural road near Piopio at about 3:30 a.m. local time after an apparent burglary at a rural farm supply store. The man fired at a lone officer, seriously wounding him, and was shot dead when a second police vehicle arrived. The child who had been with the man was taken into custody and is cooperating with police, officials said.

Acting Deputy Police Commissioner Jill Rogers confirmed the child located at the scene was receiving "wraparound support" and said two other children believed to have been with the man were still unaccounted for. When a reporter asked specifically about an unverified rumour that a baby might be among the missing, Rogers replied, "No, I'm sorry, I can't."

Detective Senior Sergeant Andrew Saunders said the immediate focus was locating the other children and retrieving them safely. "We're working hard to achieve that," he said. Police described the response as a significant operation with cordons in place and urged the public and media to respect them.

The incident followed the reported robbery of a PGG Wrightson store. Witnesses told media they saw two people flee on the back of a quad bike wearing farm clothing and headlamps. Officers found a haul of stolen items and multiple firearms on the vehicle, police said.

Police released CCTV in recent weeks of the fugitive and one of his children breaking into the Piopio Superette with an angle grinder. The footage represented the most substantive lead in a mystery that has gripped New Zealand since the children disappeared with their father in late 2021.

The deceased has been identified in media reports as Tom Phillips, who vanished from the small North Island town of Marokopa in December 2021 with his three children following a custody dispute with their mother. The children were named in court and media reports as Jayda, now about 12, Maverick, about 10, and Ember, about nine. Police and family members have said the family were believed to have been living in bushland since their disappearance despite multiple searches and a NZ$80,000 reward for information.

The mother of the children, who has been publicly identified by a single name, Cat, issued a statement saying the family was "deeply relieved" that the ordeal had come to an end while expressing sorrow at how events unfolded. She offered "aroha" to the injured officer and asked for privacy as the family worked with agencies to support the children's return and reintegration.

Police Commissioner Richard Chambers confirmed that the shot officer was conscious and speaking to colleagues. Chambers, who had been in Australia for a funeral and was due to return, described the operation as significant and said the force would not provide further immediate comment to avoid endangering the ongoing response.

Prime Minister Christopher Luxon said he had been briefed by police but did not provide any public comment on operational matters.

Authorities said the road spikes were laid after what Rogers described as "officer intuition" along a long, rural stretch of road. The chain of events — a reported theft, the quad bike sighting, a spike strip stop and the subsequent shootings — is the latest and most dramatic development in a case that has prompted repeated appeals and sporadic reported sightings over nearly four years.

Family members have made repeated public pleas for the children's safe return. In recent days, relatives had broken a long silence, with Phillips's mother and sister issuing emotional appeals. His mother said in an open letter that she loved her son and grandchildren and urged him to return so the family could provide support.

Police urged anyone with information about the whereabouts of the missing children or any aspects of the incident to contact investigators. Detective Senior Sergeant Saunders said search efforts were under way immediately after the shooting and that officers were working alongside other agencies to locate the remaining children.

The investigation will examine the theft, the weapons found on the quad bike and the circumstances surrounding the confrontation. No further operational details were released while the search continued for the two unlocated children and support was provided to the child taken into custody and to the injured officer and their family.

As the manhunt continued on Monday, police reiterated a request for public cooperation and warned that cordons and checkpoints would remain in place as officers sought to ensure the safety of the missing children and the wider community.