Purpose Manufacturing companies struggle to manage production disturbances. One step of such management deals with prioritising those disturbances which should undergo root cause analysis. The focus of this work is on two areas. First, investigating current challenges faced by manufacturing companies when prioritising root cause analysis of production disturbances. Second, identifying the stakeholders and factors impacted by production disturbances. Understanding the current challenges and identifying impacted stakeholders and factors allows the development of more efficient prioritisation strategies and, thus, contributes to the reduction of frequency and impact of disturbances. Design/methodology/approach To achieve the intended purpose of this research, a qualitative approach was chosen. A series of interviews was conducted with practitioners, to identify current challenges. A series of focus groups was also held, to identify the impacted stakeholders and factors by disturbances. Findings Various challenges were identified. These are faced by manufacturing companies in their prioritisation of production disturbances and relate to the time needed, criteria used, centralisation of the process, perspective considered and data support. It was also found that a wide range of stakeholders is impacted by production disturbances, surpassing the limits of production and maintenance departments. Furthermore, the most critical factors impacted are quality, work environment, safety, time, company results, customer satisfaction, productivity, deliverability, resource utilisation, profit, process flow, plannability, machine health and reputation. Originality/value The current situation regarding root cause analysis prioritisation has not been identified in previous works. Moreover, there has been no prior systematic identification of the various stakeholders and factors impacted by production disturbances.