The theme of natural disasters and the great impact of climate change has been gradually gaining strength within the Brazilian Public Administration in recent years. In this context, the prevention and mitigation of the effects of natural disasters have become a priority. Projects of this nature present unique characteristics, such as a high degree of uncertainty, complexity, lack of data and measurable financial return, which makes their management challenging. The methodology was based on a Unique Case Study, and the unit of analysis was the GIDES Project -Project to Strengthen the National Strategy for Integrated Management in Natural Disaster Risks. This research has the following question: Identify which characteristics of complex and uncertain project management contribute to the development of innovations to mitigate the effects of natural disasters. And, in order to achieve the general objective and its complementation according to the consecutive steps, the specific objectives of this study were: Identify the differences between traditional management tools and other ways to manage uncertain and complex projects in the context of natural disasters; Identify the elements of management of uncertain projects in the public sector in the context of natural disasters; and, identify new ideas and management technologies from international partners. As main results obtained, it was shown that the formal structure will be well used when it is specified in a planning matrix; it should have more than one management office; the integration, scope, cost, quality, human resources, communication, risk, procurement, stakeholder management is of great value coming from traditional project management; the life cycle different from the traditional way would be more beneficial in complex and uncertain projects. Apply PDIA -Problem Driven Iterative Adaptation and best fit -to the context, the stakeholders and the issue, be adaptable to changes and adjustments in procedure and protocols when appropriate. Make use of partnerships in order to generate a learning culture and as an opportunity to implement new design ideas with innovative construction, methods and management.