Background Type 2 Diabetes (T2D) is a common long-term condition affecting the health and wellbeing of New Zealanders; one in every four New Zealanders is pre-diabetic. Māori, the Indigenous people of New Zealand, are at an increased risk of developing pre-diabetes and T2D and there are significant inequities between Māori and non-Māori for T2D complications. The purpose of this study was to explore the questions of how the strengths of Māori heath organisations may be leveraged, and how the barriers and constraints experienced by Māori health organisations may be negotiated, for the benefit of Māori; and from a systems perspective, to identify strategic opportunities that may be considered and applied by Māori health organisations, funders and policy makers to respond more effectively to pre-diabetes and reduce health inequities between Māori and non-Māori. Methods Utilising case study methodology, a range of data sources were triangulated including nine semi-structured interviews, documents, and a diabetes system map to identify possible strategic opportunities for key stakeholders to respond more effectively to pre-diabetes. Results Key themes and possible actions to improve health outcomes for Māori with pre-diabetes include: (1) Recognising Māori health organisations as conduits for the community voice and influential partners in the community to effect change; (2) Strengthened partnerships with Māori health organisations for community benefit and to support measurable, evidence-based change and service delivery, particularly when Māori knowledge systems are viewed alongside a Western scientific approach; and (3) Intersectoral integration of health and social services to support provision of whānau-centred care and influence the social determinants of health and local environment. Conclusions Māori health organisations are important actors in systems seeking to improve outcomes and eliminate health inequities. Support from funders and policy makers will be required to build on the strengths of these organisations and to overcome system challenges. To realise improved health outcomes for Māori, the value placed on whānau and community perspectives not only needs to be acknowledged in the implementation of health interventions, health and social policies and funding arrangements, but performance measures, service design and delivery must evolve to accommodate these perspectives in practice.