The teenager had been under the care of Child, Youth and Family (CYF) but had been placed back in his mother's care two days before the incident.
The incident occurred when the boy refused to go back home to his mother.
The IPCA's ruling, released today, outlined the events of that night.
The summary of events said that on November 21, 2014, at about 10.36pm, police were alerted to some youths "acting suspiciously" in Waitahanui, south of Taupo.
After two officers on patrol in the area caught up with two boys in a four-wheel drive heading towards Taupo, they decided to take them home.
One of the teenagers was taken home but the other was taken to the police station after refusing to give his home address.
Despite repeated requests, the boy continued to refuse to give his address, saying that he did not want to be taken home.
Officers obtained his mother's details and address from CYF and when they could not reach her by phone decided to drive the boy there.
But when the boy was told of this arrangement, he ran into a female holding cell and refused to leave.
He told one of the officers that he did not want to go.
The officer that would later report the incident said his colleague then "grabbed [the boy] with one hand around the front of his neck or his throat and lifted him up against the wall and pushed him against the cell wall".
He said the officer said to the boy, "you're going to go home and you're going to behave" but the teenager could not talk to respond.
The officer said that when the boy was released by his colleague he was "crying and quite visibly upset and breathing really heavily".
IPCA chairman Sir David Carruthers concluded that the officer's actions in grabbing the teenager by the throat, "in the manner that he did", amounted to excessive force and were contrary to law.
The report said that when the officer was questioned about his use of force, he told the IPCA that the boy said he would "kill [him]self" before he went back to his mother's address and got "real angry".
The officer said that the teenager sprinted from the charge area into the female holding cell and put his hands and arms inside his T-shirt, so it was not possible to grab his arms.
He said the boy then sat down in a corner and would not come out.
After being called by both officers, the boy still refused and "got real abusive" and "started swearing at [them]", the officer said.
He said he went into the cell to hurry him along and said the teenager "postured like he was going to kick" him and looked like he was going to spit at him.
The officer said, in response, he "grabbed his sort of scruff of his neck, pushed him up against the wall".
He told the IPCA that he was not trying to choke him and that it was more to try and stop him from spitting. He said he was pushing his chin away rather than using force on his throat.
The report said the officer accepted that in hindsight it would have been a better option to work out a plan, with his partner and the custody officer, to remove the teenager from the cell without force.
The IPCA said: "After considering all the evidence, the Authority finds the version of events given by [the boy] and [the officer that reported the incident] to be more credible than that given by [the accused officer].
"The Authority is satisfied that [the teenager] was only verbally resisting going to his mother's house when he was grabbed by [the officer] and held against the cell wall by his throat.
"The Authority has concluded that the force used by [the officer] was excessive and not justified in the circumstances. [The officer's] actions escalated the situation rather than resolved it."
An earlier incident involving the same officer and the boy is also outlined in the report.
The first incident occurred when the boy, on the way to the police station, pulled a can of pre-mixed bourbon and coke from under his jacket.
The report said both officers asked him to hand over the can "as they were concerned it could be used by him as a weapon against them".
The officer that reported the incident said the teenager was just about to hand over the can when his colleague "abruptly pulled over, got out of the car and forcefully pushed [the boy] down on to the back seat".
The officer said his partner "was sort of holding him down trying to get the can off him".
He said the officer said to the teenager "...are you going to behave?"
He then handcuffed the teenager, and his seatbelt was put on.
The officer said his colleague's actions were "a bit excessive".
But Judge Carruthers concluded that the two officers were justified in apprehending and detaining the boy and that the officer was entitled to use reasonable force to remove the can and handcuff him in the back of the police car.
The boy said it felt like the officer was going to break his arm, the report said.
The two incidents were reported seven days after they occurred.
The reporting officer's sergeant then notified the Police Commissioner as is required by policy.
The report said the police then notified the IPCA of the incident and the authority conducted an independent investigation.
Police Area Commander for Taupo, Inspector Warwick Morehu, said this morning: "We encourage our staff to speak up if they have concerns and this demonstrates that Police will take action to question and improve its own processes; even when the individual involved makes no complaint and suffers no injury.
A Ministry of Social Development spokesperson, speaking on behalf of CYF, said the incident had been independently reviewed as determined by the police's own process.
"We have nothing to add to that," they said.
In regards to police requesting and receiving information from CYF, the spokesperson said: "Child, Youth and Family has memorandums of understanding, protocols and inter-agency agreements with a number of partner agencies and groups, including police, to help guide the way we work together, and ensure we have a collaborative approach to help children and young people be safe, strong and thrive."
