Environmental protection is one of Europe’s key values. The agricultural sector performance depends on the tax system that affects the profitability. The aim of this paper is to identify and quantify the impact of environmental instruments on the production and financial situation of the Slovak agriculture, which is expressed through the output/input and ROE indicators. The national database of Slovak agriculture provided by Radela company and environmental indicators based on Eurostat and Farm Accountancy Data Network (FADN) databases, time period 2009-2018 were examined. The used research methods were multiple regression analysis, correlation coefficient and cluster analysis. The paper defined main hypothesis, that production and financial indicators were dependent on the same variables. The results of the analysis confirmed the statistical significance of energy tax. If the percentage of energy tax in agriculture increase by 1% production would decrease by 0.01458 with a probability of 95% and ROE indicator would decrease by 2.375 with a probability of 99%. The results of the analysis confirmed stated hypothesis. The second part of the analysis deals with the hierarchical clustering. The position of Slovak agriculture across EU Member States based on two time periods 2009 and 2018 changed according the settlement of fiscal instruments.