The Managing Director/Chief Executive is responsible for the execution of the policies of the Authority and the day to day running of the affairs of the authority amongst other responsibilities.

The Authority has the following Departments: Engineering, Marine, Survey, Research, Planning and Environment, Finance, Human Resources and Administration, Corporate Affairs, Internal Audit, Legal Services, Procurement, Project Management and Special Duties, Port Services, Area Offices Co-ordination, Business Development and Inland Waterways Police Command.

Each Department is headed by a General Manager, who reports to the Managing Director/CEO.

NIWA also has a Governing Board, which supervises and drives forward the strategic direction of the Authority. The Board is headed by a Chairman.