Rozzi Phillips confirmed the death of her brother but declined to comment further.
Earlier Police Commissioner Richard Chambers confirmed a suspected burglar was confirmed shot dead by a police officer at a commercial property in Waitomo this morning.
He added the officer was shot and is in a serious condition.
A second person had been reported to be in custody, although later reports suggest they fled the scene on a quad bike.
It was earlier reported police were responding to a "serious incident" in western Waikato, near the area where police were searching for fugitive Marokopa father Tom Phillips.
Chambers said police were called to the address at about 2.30am after reports of a burglary.
It was earlier reported police were responding to a "serious incident" in western Waikato.
Phillips and his children were reported missing in December 2021.
Police commissioner Richard Chambers is set to provide more details about what happened.
But he said acting deputy commissioner Jill Rogers had travelled to the scene and would speak to reporters at 11am on Monday.
The stand-up will be held in central Hamilton.
Stuff reported Chambers had confirmed the details of the incident to staff.
The report said he acknowledged the confrontation and the officer who was shot was in a serious condition, although they were conscious and talking to fellow officers.
A resident in Marokopa said they cannot get out of the settlement because the road is closed. She was unable to get to work this morning.
A resident on Te Anga Rd in Waitomo said they heard a helicopter overhead about 4am going "low and fast".
During the response both a man and police officer were shot, he said.
Chambers said the man was given immediate first aid, but died at the scene.
Phillips and his children had been missing since December 2021.
The mother of the three children, known as Cat, shared a statement with RNZ.
She said the events this morning have brought up a wave of complex emotions.
"We are deeply relieved that for our tamariki this ordeal has come to an end. They have been dearly missed every day for nearly four years, and we are looking forward to welcoming them home with love and care."
"At the same time, we are saddened by how events unfolded today. Our hope has always been that the children could be returned in a peaceful and safe way for everyone involved.
"We express our deepest aroha to the police officer who was injured in the line of duty.
"We also extend our aroha to those in the community who have been affected, and our heartfelt gratitude to the many people who have supported us over these past four years. Your compassion has sustained us.
"As a whānau, we are now attempting to work in cooperation with the relevant government agencies to support the safe return and reconnection of our tamariki. They have endured a long and difficult journey, and we ask for privacy as we help them adjust and reintegrate into a stable and loving environment."
PGG Wrightson in Piopio has confirmed a shoot-out between police and a suspected burglar happened at its store.
Chief executive Stephen Guerin said a person broke into the store at 3.30am.
No staff were inside at the time.
He said police had full control of the scene and no staff were allowed inside.
On social media the store confirmed it was closed but said it hoped to be able to open at a later stage today.
The Waikato Times was reporting Phillips had allegedly ram raided the store, triggering the incident.
The PGG Wrightson store in Piopio has been cordoned off. Photo: Natalie Akoorie / RNZ
Phillips' father has declined to comment on the situation
Acting deputy commissioner Jill Rogers was in Waikato, and would speak to reporters in Hamilton at 11am.
Stuff reported the road was cordoned off about 10km from Waitomo Caves, and a child was seen being taken out of the area in the back of a police car.
An update from the Waitomo District Council said the road block was in place on a section of Te Anga Rd, past the Waitomo Caves between Hauturu and Waipuna Rds.
The closure was "likely to be in place for a couple of days".
Mayor of the Otorohanga District Max Baxter told The New Zealand Herald he was “getting the feeling” the incident was related to Phillips, but knew nothing more than what police had provided in their update this morning.
A resident in Marokopa said they cannot get out of the settlement because the road is closed, she was unable to get to work this morning.
A resident on Te Anga Rd in Waitomo said they'd heard a helicopter overhead about 4am going "low and fast".
They are located about 20 minutes away from Marokopa.
A school on Te Anga Rd, Piripiri School, said it hadn't been contacted by police or the Ministry of Education that would indicate that they would be affected by the incident.
Staff understood there was a road closure and some traffic was being detoured.
Asked if the incident was related to Phillips, the police media team said they did not have any further details beyond what they had issued at this stage.
Prime Minister Christopher Luxon says he's been briefed on the situation in Waikato, but he was leaving it to police to update.
