The European Commission requested scientific technical assistance for the analysis of a European Union coordinated monitoring programme on the prevalence of norovirus in raw oysters. A total of 2,180 valid samples were taken from production areas and 2,129 from dispatch centres, taken over two consecutive years, ensuring the precision and the confidence desired in the estimation. The prevalence at production areas was estimated to be 34.5% (CI: 30.1–39.1%), while for batches from dispatch centres it was 10.8% (CI: 8.2–14.4%). The analyses show a strong seasonal effect, with higher contamination in the period November to April, as well as lower contamination for Class A areas than other classes. These associations were observed in both production areas and batches from dispatch centres. The results for both genogroups were above the respective limit of quantification (LOQ) in less than 10% of the samples taken. The simple substitution of not‐detected and positive samples below the LOQ, by half of the limit of detection and half of the LOQ, respectively, produced estimates of the proportion of samples above or equal to 300 copies per gram (cpg) comparable to the statistical model. The current bacteriological microbiological criteria applicable to live bivalve molluscs might be complemented by a norovirus criterion. The analyses of the substitution approach show that selection of a potential limit within a microbiological criterion close to or lower than the LOQ (for example, less than 300 cpg, given the current test used in this survey) would be difficult to apply. This survey only assessed thresholds from the perspective of the analytical capability and not that of human health risk.