The new Industrial Emissions Act (IEA) entered into force on 1 June 2013, repealing the former Integrated Pollution Prevention and Control Act (IPPCA). The IEA transposed the requirements of Industrial Emissions Directive 2010/75/EU. The IEA applies to some 270 plants and installations across Estonia and introduces a number of changes to earlier regulation. Most significantly, conclusions regarding best available techniques (BAT) are compulsory.

According to the IEA, administrative agencies must strictly apply the requirements of BAT conclusions when issuing an integrated permit. Meanwhile, the IPPCA allowed administrative agencies to specify higher emission limits than achievable by BAT. BAT conclusions must be adopted as an implementing decision under a regulatory procedure in line with Article 75 of Directive 2010/75/EU. These decisions are implementing acts within the meaning of Article 291 TFEU, so that administrative agencies issuing integrated permits must follow the requirements of BAT conclusions even if these requirements have not yet been transposed into national law.

The European Commission adopted four BAT conclusions as implementing decisions in 2012–2013. Under Article 13 (7) of Directive 2010/75/EU and Section 166 of the IEA, BAT reference documents adopted by the European Commission will apply as BAT conclusions until decisions of the European Commission containing BAT conclusions enter into force. An additional BAT conclusion concerning shale oil production is established by an order of the Estonian Minister of the Environment.