The article deals with a topical issue – a proposal for EU Regulation on plants obtained by certain new genomic techniques (NGT), and its planned provisions which crosscut several regulatory areas of biotechnology, the internal market, food and agriculture. The investigated draft of a new EU economic and environmental legislation is currently in the pipeline of the EU legislative process and subject of an inter-institutional trilogue between the Commission, the European Parliament and the EU Council due to many related regulatory controversies. The paper explores those controversies and appraises possible legal and economic consequences of the proposed solutions. The article argues that the proposal introduces a far-reaching normative deregulation and an unjustified complexity of legal provisions, which may instigate further polarization of national positions of the EU Member States regarding the use of NGT plants, techniques and derived products, as well as a decrease of legal coherence and certainty in the field concerned.