Te Arawhiti, the Office for Māori Crown Relations, has confirmed it will disestablish 49 roles as it narrows its focus on Treaty claims and coastal rights.
Nine new roles are being created, with staff affected by the restructure given the first opportunity to apply for new and vacant positions.
Interim chief executive Anaru Mill said 28 of the 49 roles set to be axed were already vacant - and nine new roles will be created.
Affected staff will have the first option to apply for new and vacant positions.
Māori Development Minister Tama Potaka in August revealed plans to redesign what has been known as the Office for Māori-Crown Relations, by transferring the Māori-Crown Relations functions to the Māori Development agency, Te Pūni Kōkiri.
Some 44 full-time equivalent roles will be transferred to Te Pūni Kōkiri from 24 February.
Other functions being transferred include monitoring and reporting on the implementation of Treaty settlements, leading post-settlement relationships, coordinating significant events on behalf of the Crown, providing strategic advice on the distinct rights, interests, and responsibilities of iwi, hapū and Māori, and ensuring the public service can effectively engage with Māori.
Te Arawhiti has had two ministers, but after the transfer will report only to Treaty Negotiations Minister Paul Goldsmith and will focus on the Takutai Moana foreshore and seabed claims, and resolving historical Treaty of Waitangi claims.
The government is planning changes to the Takutai Moana legislation, restricting the ability to claim customary marine titles.
Te Arawhiti began consultation on the role and function changes last month, envisaging a cut of 51 roles.
Chief executive Anaru Mill in a statement said staff had made 74 submissions on the changes, with 54 of those focused on the redesign of the ministry.
"I want to acknowledge how challenging this process has been for our staff, particularly those who have been impacted by the change proposals and today's final decisions," Mill said.
He said staff moving to Te Pūni Kōkiri would retain pay and conditions no worse than their previous roles.
"To make these changes successful for Māori and the Crown, we will need to stay in lockstep going forward. It's important that iwi Māori have confidence in the government's ability to collectively uphold their Treaty settlements, rights and interests, and that we can demonstrate what it takes to uphold the mana of the Crown."