The CEI is structured into 10 regional inspectorates, two branch offices and directorate; As of 31 December 2019, there were 556 employees approx. 80% of whom are inspectors.
Regional inspectorates in:
Praha, České Budějovice, Plzeň, Ústí n/Labem, Liberec, Hradec Králové, Havlíčkův Brod, Brno, Olomouc, Ostrava; branch offices in Zlín and Karlovy Vary.
The Director of the CEI is appointed by the Minister of the Environment.