The purpose of this study was to report data analysis results from the International Health Regulations (2005) Ship Sanitation Certificates (SSC), recorded in the European Information System (EIS). International sea trade and population movements by ships can contribute to the global spread of diseases. SSC are issued to ensure the implementation of control measures if public health risk exists on board. EIS designed according to the World Health Organization (WHO) “Handbook for Inspection of Ships and Issuance of SSC”. Inspection data were recorded and SSC issued by inspectors working at European ports were analysed. From July 2011-February 2017, 107 inspectors working at 54 ports in 11 countries inspected 5579 ships. Of these, there were 29 types under 85 flags (including 19 EU flags). As per IHR (2005) 10,281 Ship Sanitation Control Exception Certificates (SSCEC) and 296 Ship Sanitation Control Certificates (SSCC) were issued, 74 extensions to existing SSC were given, 7565 inspection findings were recorded, and 47 inspections were recorded without issuing an SSC. The most frequent inspection findings were the lack of potable water quality monitoring reports (23%). Ships aged ≥12 years (Odds Ratio, OR = 1.77, 95%Confidence Intervals, CI = 1.37–2.29) with an absence of cargo at time of inspection (OR = 3.36, 95%CI = 2.51–4.50) had a higher probability of receiving an SSCC, while ships under the EU flag had a lower probability of having inspection findings (OR = 0.72, 95%CI = 0.66–0.79). Risk factors to prioritise the inspections according to IHR were identified by using the EIS. A global information system, or connection of national or regional information systems and data exchange, could help to better implement SSC using common standards and procedures.