Introduction Despite the public health system’s critical role in non-communicable disease (NCD) surveillance in Vietnam, limited evidence exists on the implementation of NCD surveillance activities within these systems and the need for capacity building across different system levels to meet expected NCD surveillance goals. This study aimed to evaluate the status of and describe factors affecting the implementation of NCD surveillance activities and to identify the NCD surveillance capacity building needs of the public health system in Vietnam. Methods We used a mixed-methods approach in four provinces, conducting self-completed surveys of staff from six Preventive Medicine Institutes (PHI), 53 Centres for Disease Control (CDC) and 148 commune health stations (CHS), as well as 14 in-depth interviews and 22 focus group discussions at four PHI, four CDC, and eight district health centres and CHS. Results Study findings highlighted that although Vietnam has a well-functioning NCD surveillance system, a number of quality issues related to NCD surveillance data were salient. Multifactorial reasons were identified for incomplete, unconfirmed, and inaccurate mortality data and current disease surveillance data. Data on NCD management and treatment were reported to be of better quality than data for screening, targeted treatment, and counselling communication. Main factors affected the effective implementation of NCD surveillance, namely lack of complete and specific guidelines for NCD surveillance, limitations in human resource capacity within NCD departments, and shortage of funding for NCD surveillance activities. Conclusion Study findings provide practical strategies for strengthening health system capacity for NCD surveillance through developing policies, guidelines, and standardised tools to guide NCD surveillance and a road map for integrated NCD surveillance, developing training packages and manuals for all levels of the health system, and conducting utilisation-focused surveillance training programs.