Purpose The purpose of this paper is to identify the critical challenges in the implementation of cloud enterprise resource planning (ERP). The challenges identified were customization, organizational change, long-term costs, business complexity, loss of information technology competencies, legal issues, integration, data extraction, monitoring, migration, security, network dependency, limited functionality, awareness, performance, integrity of provider, perception, and subscription costs. Here the small and medium enterprises (SMEs) and large organizations were differentiated with respect to the challenges identified. This paper also suggested ranked lists of challenges both for SMEs and large organizations. Design/methodology/approach An online survey was conducted and data of 93 respondents were analyzed. Exploratory factor analysis and one-way analysis of variance (ANOVA) was used to statistically test the data. Here the SMEs and large organizations were differentiated with respect to the challenges identified. Findings This study shows that SMEs and large organizations differ from each other for most of the challenges except business complexity, integration, monitoring, security, limited functionality, performance, and integrity of provider. Also from the ranked list of challenges in cloud ERP, security was the top concern for both SMEs and large organizations. Originality/value The findings may help organizations to get a broad idea about the challenges which are critical for the implementation of cloud ERP.