Mr Comer told TVNZ he had been speaking to staff about the aims and ambitions for the department under the new Government.
" ... I did say to them we would have to do this with fewer resources".
Maori Affairs Minister Pita Sharples said Te Puni Kokiri staff had been briefed on "efficiency" measures.
"How the ministry manages their fiscal pressures and efficiency dividend is, of course, an operational matter for management. I expect to be consulted on the chief executive's proposals for how Te Puni Kokiri continues to deliver the most effective services to the public, within the budget they have been allocated," he said.
Ms Pilott said the cuts would impact heavily on the advocacy, social and development work the agency did on behalf of Maori.
"TPK provides a Maori perspective on all policies that Government is considering and its regional networks are important in keeping that advice grounded. Just this week we have seen TPK move quickly into action over issues to do with Treaty principles and asset sales," she said.