Manufacturers are increasingly adopting manufacturing data analytics (MDA) as a key factor for smart manufacturing. However, successful MDA implementation remains limited due to various issues. Existing studies have barely suggested a comprehensive such issues by focusing on parts of technological, organizational, and environmental (TOE) contexts or issues limited to partial steps of MDA. This study addresses these gaps by identifying comprehensive issue set for MDA implementation (CISM) through a systematic review of 35 papers. The 29 distinct issues with 9 categories were derived to cover both TOE contexts and the five major steps of MDA. The comprehensiveness of CISM was validated through three real-world MDA implementation case studies. CISM is expected to suggest issues for manufacturers to address proactively in MDA implementation and to serve as a basis for stimulating future studies on MDA implementation. • Manufacturers are increasingly attempting to implement manufacturing data analytics (MDA). • Existing studies rarely offer a comprehensive set of issues for MDA implementation. • This study constructs a comprehensive set of 29 issues for MDA implementation across TOE contexts and the 5 major MDA steps • CISM utility was validated with three real-world MDA case studies. • CISM will support manufacturers identify and address key issues in implementing data-driven cyber manufacturing.