Police located the boys after father-of-two Arun Kumar was found stabbed in the Railside Dairy on Great North Rd in Henderson about 7.30am yesterday.
The schoolboys were also being quizzed about a spate of aggravated robberies, the Herald understands.
Mr Kumar, 57, was stabbed in the neck in front of his wife during what is believed to have been an attempted robbery of the Henderson dairy.
As tributes were paid last night to Mr Kumar - known for his humbleness and generosity to children in need - the 12- and 13-year-old were in CYFS custody ahead of a court appearance this morning.
The Herald has learned that before the fatal incident there had been a spate of similar robberies and attempted robberies in the Henderson and Ranui area. It is understood police are investigating whether the youths were involved. "All possibilities are being explored," said Detective Inspector Bruce Scott, who is heading a homicide investigation into Mr Kumar's death.
Henderson residents yesterday told the Herald about a group of young teens who had been terrorising the neighbourhood.
John Tuapiki lives near the Railside Dairy and visited the bakery next door about 20 minutes before Mr Kumar died. He said a youth had been threatening people near the dairy with a large knife on Monday afternoon, asking for cigarettes.
A teenager said he was attacked by youths demanding cigarettes across the road from the dairy.
He was punched to the ground by one while another tried to steal his cellphone. They threatened to stab him and his girlfriend before "gapping it" when an adult pulled over in a car.
Police said the 12- and 13-year-old were being interviewed in the presence of support people.
Mr Scott said Mr Kumar's wife was unhurt but was traumatised and was being helped by Victim Support and a police ethnic liaison officer.
Shirlyn Prasad Kumar, the daughter of Mrs Kumar's cousin, said Mr Kumar was a good man.
"We have known them for many years, even before they migrated to New Zealand from Fiji. I feel for his wife and daughter and son," she said.
"They were a close family, always visited family together and socialised. He was a hardworking man, a great husband and a father. A man so kind and humble, he did not deserve this."
Friend Rohitesh Prasad said Mr Kumar's death was a "tragic end to a great guy".
"We have lost a very kind, generous and humble person today," he said. "I studied aircraft engineering in New Zealand and went back to work in Fiji in 1991 where I rented his house for four years and found Arun and Anita to be very humble and generous. I last met him by coincidence at a Diwali function in West Auckland and that was after so many years.
"God give Anita strength and may his soul rest in peace."
Emergency services were called to the scene at 7.29am but paramedics could not save Mr Kumar.
The alleged offenders were not at the scene but it is understood police located them soon after.
"It's shocking to us that kids so young could be involved," Mr Scott said.
He would not be drawn on what weapon was used to stab Mr Kumar, citing operational reasons.
"A scene examination at the shop is under way and, as part of the inquiry, officers have been speaking with a number of people who were in the area at the time of the attack," he said.
"CCTV footage from a number of stores, including the dairy, is also being gathered and will be reviewed throughout the course of the inquiry."
Lawyer Bernie Allen, from a nearby law firm, said he always bought his supplies from the dairy, and staff were shocked by news of the stabbing.
"They were the most beautiful couple you could ever meet," he said.
"We're feeling deeply for his wife. It's too early to understand it all but we feel like our precinct, our people have been violated.