Chair Mana Tahere said the delegation would not sit in the room in silence with a government it said was running roughshod over Māori.
There was frustration and dissatisfaction over the way the government is treating Māori, he said.
Ngāpuhi is an iwi associated with the Northland regions, centred in the Hokianga, the Bay of Islands and Whangārei.
Tahere cited issues such as Māori wards, changes to the (Ministry for Children) Oranga Tamariki Act, moves to overturn the seabed and foreshore judgement and the forthcoming Treaty Principles bill.
Tahere said Ngāpuhi wanted to exclude the government from meetings until further notice.
Ngāpuhi will lead a hikoi in Kaikohe on Saturday calling for devolution of Oranga Tamariki resources to iwi to address the overrepresentation of tamariki Māori in state care and is holding a rally at Parliament on Monday.
The meeting was part of a National iwi Chairs Forum on Wednesday morning in Tamaki Makaurau/Auckland attended by a number of government ministers.
They included Luxon, Minister of Justice Paul Goldsmith, Minister of Māori Development Tama Potaka, Customs and Associate Health Minister Casey Costello and Climate Change Minister Simon Watts.
Te Rūnanga o Ngāti Whātua is taking the government to court over its plans to overturn a judgement that lowered the threshold for recognising customary rights to the foreshore and seabed.
It was one of the government actions the Ngāpuhi leaders cited for their walkout.
Goldsmith wants to go back to how things were before the Court of Appeal decision, where Māori wanting Customary Marine Title need to prove they have had continuous exclusive use and ownership of an area since 1840.
Rūnanga co-chairs, Reverend John Marsden and Dame Rangimarie Naida Glavish, say it is an arbitrary decision, and exposes the government's contempt towards its Treaty partner.
In a statement, a spokesperson for Luxon called the meeting "positive, robust and honest dialogue".
"The Prime Minister continues to welcome constructive dialogue with Iwi leaders and recognises the significant and positive contribution that Iwi are making to our country.
"The Government is focused on turning around years of decline in Māori outcomes, particularly in health, education, employment and housing, overseen by the previous government."
- with reporting from Te Ao Māori News
