First decade of 21st century raised new issues for development of national economies connected with increased volumes and complexities of international trade, new business models and requirement, however also security threats and organized crime vulnerability also increased. From 2004 Latvian customs is working in new environment as a part of integrated European Union customs facing complex fraud and security problems and acting as a part of integrated European external border. In the European Union environment customs is facing with considerable demands for trade facilitation and protection of vital interests of the society. On the one hand this means need for effective security and control of international supply chains while on the other hand there are legitimate trade facilitation issues. The paper is devoted to the new challenges of Latvian Customs Administration acting in customs union environment, as well as targets and tasks for State Revenue Service are contemplated. Research on professional competences of customs authorities’ officers and regulations is conducted. Latvian example of implementation of procedures and innovative educational technologies with main objective to increase the capacity of customs administrations is described. According to the results of the research recommendations for future Latvian customs administration and for improvement of Latvian customs education system are worked out.