This paper examines Special Tariff System (tokubetsu kanzei seido) and its role in the system of trade remedies in Japan. By particularly focusing on measures of anti-dumping, countervailing, emergency, and retaliatory duties the authors implement a comprehensive analysis on both theoretical background and empirical case studies of application of the Special Tariff System and identify peculiar features of its regulation by government authorities. This paper argues that the specificity of Japan’s Special Tariff System is mainly expressed in its institutional context, comprising of salient state regulation, lack of legal transparency and dispersion of the regulating acts on trade remedies in the system of Japanese legislation, pluralism of regulatory authorities and overlapping of their jurisdiction in managing the application of such measures. In addition, this paper provides a systematic view of current legislation on trade remedies in Japan and aims to identify the reasons of infrequent practical application of the Special Tariff System. The authors conclude that bureaucratic barriers, low integrity of the legislation on trade remedies, lack of cooperation between regulatory authorities, resource-based structure of Japanese import are the factors accountable for the infrequency of practical application of the System. Nevertheless, due to the increased import of goods from emerging economies in recent years, namely from China, Republic of Korea, and Taiwan, there is a high probability that the sphere of application of Japan’s Special Tariff System might be extended.