The lack of systematic work to determine the level of development of the competencies of state civil servants in the field of information security in the context of digitalization increases the risks of the Russian state authorities in this area. The existing gaps in legislation, in methodological support from regulators, in the practice adopted in the civil service, and the relevance of the problem, confirmed by the federal project "Information Security", led to the need to develop a standard assessment tools and methods for assessing the competencies of state civil servants in information security. The article describes the scientific and practical approaches to the development of the methodological apparatus of assessment and the results of its pilot implementation in 2019–2020. The article describes the scientific and practical approaches to the development of the methodological apparatus for assessing competencies in information security and the results of its pilot implementation in 2019–2020. The subject of the research is methodological tools, including evaluation tools (tests, cases), methods and procedures for organizing the assessment of information security competencies for evaluating candidates and employees. The results of the analysis of foreign practices, the survey of the demand for methodological tools in government bodies, the analysis of the regulatory and methodological support for the assessment of information security competencies are presented. This conceptual approaches to the development of competency models, assessment tools and assessment procedures taking into account the requirements of normative acts in the field of information security, the characteristics of the target groups of employees estimated and evaluation purpose. The approbation of the methodological apparatus confirmed its practical value for the authorities. It is assumed that the use of methodological tools will make it possible to obtain the necessary analytical information to determine the tasks and select programs for the development of competencies, which may also be in demand in educational organizations engaged in the training of state civil servants.