This study aimed to assess the implementation of the MDSR system. The mixed cross-sectional study was conducted in 12 regions. The quantitative analysis used ordinal intervals: Excellent, Good, Satisfactory and Poor. Qualitative analysis developed themes to inform MDR system implementation. The findings showed that leaders were following up at the health facility, the community, and individual clients. The system implementation at the regional level was Satisfactory (75–84%), and at the district and health facility level was Poor (below 75%). Generally, responses to the action plan at all levels studied were rated Poor. The timeliness of notification to MD was found to be Satisfactory (75–84%) in three regions and Poor in Dar es Salaam and Mwanza. The daily notification of MDs was 57.3% of the 349 weekly reports. The completeness variables improved significantly to Excellent scores (above 95%) after a week, but not for notifications. Therefore, the system produces data that goes beyond numbers, thereby making it not inferior. The system generates MD data through timely notifications and weekly reporting, with the latter yielding twice as much.