Article 16 of the EU ETS Directive establishes a limited harmonisation of the financial penalties that will be paid by operators that fail to surrender the necessary number of emissions allowances (i.e. €100 per tonne of CO2).

More generally, the co-legislators decided that the Member States should adopt rules on penalties for breaches of national legislation which transpose the Directive's requirements and that these penalties should be "effective, proportionate and dissuasive".