Pere walked out of the house willingly and lay face-down on the front lawn while plastic restraints were attached to his hands.
Acting Assistant Commissioner Investigations Glenn Dunbier said when officers moved forward to lift Pere to his feet, a Bushmaster rifle carried by an AOS member accidentally discharged.
Pere suffered a single gunshot wound to his upper right middle back region.
He was immediately given first aid and was taken to Hawkes Bay Hospital by ambulance, before being transferred to Wellington around 10pm.
Dunbier said Pere's actions had not contributed to the shooting.
The officer who shot Pere was "extremely upset", he said.
"The officer involved is understandably extremely upset by what has happened and we have support mechanisms in place for him. He is more concerned about Mr Pere's condition.
"This is a terrible tragedy and we will be conducting a thorough and robust investigation into what took place and how the firearm came to be discharged in such a manner."
Dunbier said he could not confirm why the firearm was discharged and whether it was human error or a firearm malfunction.
"We have a lot of work to do over coming weeks to determine exactly what happened and how it happened."
Detective Superintendent Paul Kench of Wellington is set to head the internal police investigation into the incident.
A St John Ambulance spokesman refused to give details about the incident, telling the Weekend Herald that police had instructed them not to.
A neighbour said she heard a loud "bang" but didn't know what happened until she saw an ambulance arrive and armed police outside.
"The house is still locked down," the neighbour said.
Police shootings
• July 2013: Former soldier Caleb Henry is shot dead by police on the Northern Motorway after a 350km pursuit.
• June 2013: Burglar Adam Morehu, 33, is shot dead by police in New Plymouth. Police fired after Morehu threatened to kill two officers.
• 2011: Lachan Kelly-Tumarae, 19, dies after being shot by police in a stand-off in Hawkes Bay. An investigation last year found police actions were justified.
• 2009: Halatau Naitoko, 17, is accidently shot dead by police pursuing another man in Auckland.
• 2000: Steven Wallace is shot by police after a window-smashing rampage in Waitara.
- Additional reporting: Vaimoana Tapaleao