IIWM is governed by the Trust Deed as registered in November 2011. The institute became an independent organisation after being a project of the Science and Technology Department. This enabled the institute to receive funds from Madhya Pradesh Government after meeting its overheads.
IIWM commenced various other projects and activities in the neighbouring states and gradually became a Pan India entity. Today, the institute has its Headquarter in Bengaluru with branch offices in Bhopal, New Delhi and Meghalaya. Apart from this, the organisation receives funds not just from the Government, but also from international institutions, corporate bodies and other institutions.
The management of affairs of the organisation is vested with Board of Trustees, which is the ‘Governing body’ of the institution. The 'Board of Trustees' has formulated a ‘Governing Council’ to steer the overall governance and have a better control over the functioning of the institution. For monitoring and executing the day-to-day operations of the institution, an Executive Director is appointed, who is a member of the Governing Council and reports to the Board of Trustees. The Governing Council and the Board of Trustees, especially the Managing Trustee supports the organisation as and when required by the Executive Director. A Financial Secretary is nominated by the Board of Trustees to oversee the financial aspects of the organisation. The technical matters of the organisation and the projects and programmes and the staff are governed by the Executive Director.
The organisation has an Oversight Mechanism, Procurement Policy, HR Policy, Code of Conduct, Operations policy, Training and Capacity Building Policy, Sexual Harassment Policy, Environmental Policy, Climate Change Mitigation Policy, Governance Statements, Financial Auditing Procedures and other governance structures in place which meets the National and International Standards.