The competent authorities of the Member States of the European Union are required to perform animal welfare inspections on livestock farms. The data obtained from these official inspections performed in Finnish cattle and pig farms in 2010–2015 were used with the aim of estimating the prevalence of the most common non-compliances and identifying underlying risk factors. The prevalence of non-compliant cattle and pig farms was 24.2% and 27.9%, respectively. In cattle, the most common problem was an inadequate lying area followed by deficient housing conditions for calves; in pigs, it was a lack of enrichment material. The non-compliances concerning cattle were most frequently detected in autumn and in farms with small herd size, with tie-stall housing and outdoor rearing year-round. The pig farms with a farrow-to-finish unit had a higher prevalence of non-compliances than other production types. The prevalence of the non-compliant farms differed notably between the regions. It can be concluded that the cattle welfare inspections should be performed with a focus on the cold and rainy seasons and at small farms, whereas the pig welfare inspections should mainly focus on farrow-to-finish units. The data received from official inspections should be efficiently utilized in the development of animal welfare inspection system, with the aim of risk-based, consistent and uniform inspections. In addition, the data should be utilized in targeting information for farmers.