The aim of the article was to evaluate production efficiency changes of agricultural enterprises specialized in livestock production and identify its determinants. The total factor productivity (TFP) was used to analyse the changes as determined by the DEA Malmquist index. Evaluated sample contained panel data of 440 farms (114 organic and 326 conventional) based on FADN survey in the period 2011 - 2015. The results showed very little difference in technical efficiency between groups and relatively negligible changes over the time. About 69% of organic farms reached the productivity growth with the change in TFP of 3.17%. A total of 59% of conventional farms were managed with increasing productivity and the TFP change by 1.48%. Differences between groups were given mainly by Utilized agricultural area per farm, level of Total production, Livestock output, sum of Current subsidies per hectare, and by FNVA / AWU.