Reyes was sworn as national defense secretary two days after retiring as the AFP's 27th chief of staff. In concurrent capacity, he also chaired the National Disaster Coordinating Council. Under his leadership, he was able to imbibe a culture of excellence at the department of national defense and transformed it into a technology-driven defense establishment making it more responsive to the challenges o rapidly changing security establishment amidst the rising trend in global terrorism, He was instrumental in crafting the National Internal Security Plan which is now being implemented by the government in addressing the root causes of insurgency through poverty alleviation, delivery of basic services and empowerment of the local government.