Throughout its existence, the Goto clan, who were classified as to-doma daimyo, assumed the role of the domain's ruler, overseeing various aspects of governance and administration within the region.

[1][2] In the han system, Fukue was a political and economic abstraction based on periodic cadastral surveys and projected agricultural yields.

The early days of the domain were troubled by political problems, with rivalries between different factions of the ruling clan, violent clashes over fishing rights between various islands and villages, and the unpopular suppression of the Kirishitan religion per the Tokugawa bakufu's national seclusion policies.

The situation became more quiescent in the 18th century with increasing prosperity due to the growth of whaling and the establishment of the separate Tomiei sub-domain (3000 koku) on Shinkamigotō.

He arrived in Kyoto in 1868, and the new Meiji government ordered him to strengthen the maritime defenses of his island domain against possible incursions by foreign ships.

The kokudaka, or stipend of the domain, amounted to 3000 koku, and Goto Morikiyo was recognized as a koke and kotaiyoriai, which signified his status as a daimyo within the feudal system.

Moving forward to the time of the 7th head, Morinuki Goto, who served as an aide to Shogun Iemochi Tokugawa, the family's actual income exceeded 10,600 koku.