Two proposals were made to staff today.
One would see a transfer of functions to Te Puni Kōkiri, the government's principal policy adviser on Māori wellbeing and development, with 44 employees transferred.
The second would see a redesign of Te Arawhiti to focus solely on Treaty settlements and Takutai Moana Claims under which 51 roles would be cut and eight new roles established.
Staff have four weeks to provide feedback on the proposals.
Te Arawhiti - the Office for Māori Crown Relations - will focus on its legislative functions to progress settlements under Te Tiriti o Waitangi and the Marine and Coastal Area (Takutai Moana) Act.
Te Puni Kōkiri will take over the post Treaty settlement implementation function and other functions.
Te Kaihautū Māori for Te Pūkenga Here Tikanga Mahi Public Service Association, Janice Panoho, said the "flawed" plan would be a significant setback for Māori Crown relations.
"Te Arawhiti is left doing important work but will have far fewer people to carry out these vital functions, which flies in the face of the government's commitments to progressing Treaty settlements.
"The government promised to listen to the evidence, but again it's ignoring the advice of those working at the heart of Māori Crown relations."
Documents released under the Official Information Act show Te Arawhiti chief executive Lil Anderson warned the government in July this year that the benefits of the reducing overlap between Te Arawhiti and Te Puni Kōkori were "overstated".
Panoho said the chief executive warned the government at the time that the the proposal "would risk government failure to achieve its Treaty settlements and Takutai Moana programme" by separating implementation from negotiation.
"This shows how flawed the plan is. The whole point of Te Arawhiti was to be a one-stop shop for accelerating treaty settlements, supporting Māori in the future so Treaty settlement commitments were implemented and strengthening the public service capability around the Treaty."
Data shows just over 2000 jobs were lost from the public service between December 2023 and June this year.