The performance of publicly funded canal irrigation systems or more commonly called national irrigation systems (NIS) in the Philippines remained below expectations despite considerable system rehabilitation and improvement efforts. The continued suboptimal performances were attributed to technical, managerial, institutional and policy issues and constraints, and in recent years, to climate change. Irrigation modernisation is recognized as strategic option to improve the irrigation system performance. It is defined as a process of technical, management and institutional transformation to improve irrigation services to farmers. The main objective of the research study was to formulate a strategy for developing a modernisation plan for national irrigation systems in the Philippines. The research methodology was framed with deliberately selected assessment and characterization procedures, which were adoptively modified and integrated to critically analyse the state of coherence among the three fundamentals of irrigation system water delivery: design, operation and water supply; and to identify solutions for any inconsistency. It included, among others an analysis of the process, nature and impacts of rehabilitation projects; diagnostic assessment of the irrigation systems; revalidation of design assumptions on water balance parameters; characterization of irrigation management, service and demands; and identification of options for improvements. The developed methodology for examining the different aspects of planning and operations of NIS with an end view of modernising the systems provides a more comprehensive and applicable methodology for drawing up of a more relevant plan for NIS modernisation. The knowledge gained on case study systems provides a sound basis for planning of appropriate modernisation solutions for the case study systems and in cases of ungauged, small-scale NIS. The methodology developed in this study could serve as a blueprint for modernisation program for NIS.