The article describes the requirements for the training of maritime industry specialists, which are regulated by programs and courses approved in accordance with the minimum standards of competency of the International Convention on Standards of Training, Certification and Watchkeeping for Seafarers. In the context of the implementation of the Manila amendments 2010 to the system of maritime specialists training, the priority task is to achieve a qualitative new level of training of maritime specialists, the use of educational resources of a new generation, adapted to the goals and objectives of the professional training of maritime specialists. In the context of the identified issues in the article the features of the organization of e-learning on LMS Moodie in the Kherson State Maritime Academy are revealed. The organization of the assessment system for cadets in the academy which includes compulsory computer testing on LMS Moodie is presented in detail. It is shown that creation of a system for assessing the formation of professional competency of future maritime specialists by means of web technologies is a powerful mechanism for introducing a competency approach in higher maritime education. Analyzing the role of the cognitive component as the basic element of professional competency, it is proposed to include it in the criteria for assessing the indicators of the competency level formation. The use of the LMS Moodie Learning Management System to assess the cognitive component of professional competencies in higher maritime education is considered. The elements of the organization of formative assessment in electronic courses are offered in line with modern world trends in e-learning. On the example of using the LMS Moodie repository of competencies in the Kherson State Maritime Academy in the preparation of future navigators, it was concluded that the assessment of maritime specialists professional competencies is differ from the traditional assessment and has the further perspectives for the organization of the educational process at the institution.