Current article sets out a scientific debate on the phenomenon of innovation security (IS) and regional IS in particular. Authors suggest that IS should be considered as an independent type of regional security, along with economic, environmental, political, etc. security types. It is assumed that IS is one of the key imperatives of regional development along with the sustainability, competitiveness, and innovativeness.Article rests upon the analysis of the mechanisms and tools within the innovation policies of the highly innovative countries of the Baltic region - Denmark, Finland, Germany, Norway, and Sweden, which demonstrate an “unintended” application experience of the regional IS provision. The study underlines the most influential factors affecting the institutional framework of an IS establishment process. Paper concludes with a set of policy recommendations on regional IS in the context of contemporary socio-economic trends.