The most high-profile incident occurred on April 15 where shots were fired inside the Sofitel Hotel foyer in Auckland CBD after growing tensions between the two gangs.
McNaughton said although no one was injured, their actions were extremely serious and there was a significant risk to members of the public.
The elaborate Police operation involved a number of staff from across Tamaki Makaurau, Northland and the National Organised Crime Group who have been working tirelessly over the last two months to identify all individuals involved in these series of incidents and hold them to account, he said.
The investigation also uncovered a number of people who were allegedly assisting the offenders involved who were actively attempting to avoid Police.
Three firearms including a prohibited semi-automatic rifle, a sawn-off shotgun as well a large amount of ammunition and improvised explosive devices were also seized as part of the operation,
Seven Mongols gang members or associates have been charged with a range of serious offences including participation in an organised criminal group, dangerous act with a firearm with intent to cause grievous bodily harm, arson and possession of firearms and explosives, and drug dealing.
Six Head Hunters gang members have also been charged with participating in an organised criminal group, dangerous act with a firearm with intent to cause grievous bodily harm, possession of firearms and drug dealing offences.
Six others linked to the Head Hunters gang have been charged with accessory after the fact in relation to allegedly assisting an offender involved in the Sofitel shooting to escape Police.
"While the series of incidents were targeted between members linked to both gangs, the actions of those involved posed a serious risk to the safety of the wider public," Naughton said.
"Gun violence has no place in our society and we hope the conclusion of this operation reassures the public that dangerous and serious criminal acts by gangs will not be tolerated by Police."
McNaughton is not ruling out further charges.