Top-ranking Māori officer Superintendent Wally Haumaha says it has been acknowledged that there could be some unconscious bias in the police force, but anyone that isn't acting appropriately will be discovered.
Statistics New Zealand figures show the number of youth facing charges in court has halved in the past six years. However in 2008, the number of young Māori under 17 years old facing charges in court was 48% and in 2013 it rose to 58%.
Julia Whaipooti of legal lobby group JustSpeak, says the drop in youth appearing in court is because of pockets of change in the system - but unfortunately for Māori, the gap has grown.
Ms Whaipooti, of Ngāti Porou descent, works in the community and says she sees institutional racism first hand. Bias against Māori has not been admitted by everyone in the justice system, she believes.
"I think the biggest barrier, though, is accepting or acknowledging that there is institutionalised racism and I think it's the word racism that gets people politically scared.
"But looking at the statistics for the same offence, Māori are five times more likely to be prosecuted than non-Māori, and when we are looking at those statistics and those facts, they are not being accepted that there is something wrong within the system."
The Minister of Māori Development, Te Ururoa Flavell, agrees. He says it's not just him saying there is institutional racism, there has been much research nationally and overseas which backs this up.
Mr Flavell said he has had formal and informal discussions with members of the police.
"They recognise there are some issues to be addressed at the highest level, and we need to move towards addressing these sorts of issues - but not just put it at the hands of the police, we are talking about the system across the board."
The Māori Party has talked about a review of the whole justice system and that is probably the only way we are able to do it, he said.
Superintendent Wally Haumaha, deputy chief executive Maori, says Police Commissioner Mike Bush has recognised that there could be issues of unconscious bias in the force.
"This is a conversation that happens across society and the country, and there are issues where institutions have been cited around these areas. But if I look at the overall police values, we have added on top of the others diversity and empathy," Mr Haumaha says.
If anyone in the force isn't acting appropriately, they will soon be discovered, he says.
"We have some very excellent people in the organisation now who are aware of all these issues and the accountability has probably never been higher in terms of a police officers' actions.
"So whilst there might be individuals, the New Zealand Police doesn't advocate any form of racism whatsoever."
In 2012, police put the Turning of the Tide Strategy in place, which aims to bring down the over-representation of Māori in the justice system. The strategy aims to decrease the proportion of first-time youth and adult offenders who are Māori by 10%.