The Malaysian government has encouraged public sectors to adopt innovation to create value added that will increase their wealth creation and to enhance their competitive advantage. There are many initiatives have been put forward to encourage the innovative activities, nonetheless, the efforts are rather less fruitful. Thus, this paper aims to discuss the challenges faced in managing non-technological innovation in the organization and suggest ways for improvement particularly in Malaysian public sectors. For that purpose, seven interviewees have been chosen to be interviewed using semi-structured questions from two categories; facilitator and implementer. Thematic approach is implemented to analyse the data collected. This study has identified three critical challenges, which include innovative culture, inadequate resources and lack of collaboration with other institutions.