Under the early courts, when military conscription had been centrally controlled, military affairs had been taken out of the hands of the provincial aristocracy. But as the system broke down after 792, local power holders again became the primary source of military strength. Shoen holders had access to manpower and, as they obtained improved military technology (such as new training methods, more powerful bows, armor, horses, and superior swords) and faced worsening local conditions in the ninth century, military service became part of shoen life. Not only the shoen but also civil and religious institutions formed private guard units to protect themselves. Gradually, the provincial upper class was transformed into a new military elite based on the ideals of the bushi (warrior) or samurai (literally, one who serves.

Bushi interests were diverse, cutting across old power structures to form new associations in the tenth century. Mutual interests, family connections, and kinship were consolidated in military groups that became part of family administration. In time, large regional military families formed around members of the court aristocracy who had become prominent provincial figures. These military families gained prestige from connections to the imperial court and court-granted military titles and access to manpower. The Fujiwara, Taira, and Minamoto were among the most prominent families supported by the new military class.

Decline in food production, growth of the population, and competition for resources among the great families all led to the gradual decline of Fujiwara power and gave rise to military disturbances in the mid-tenth and eleventh centuries. Members of the Fujiwara, Taira, and Minamoto families--all of whom had descended from the imperial family--attacked one another, claimed control over vast tracts of conquered land, set up rival regimes, and generally broke the peace of the Land of the Rising Sun.

The Fujiwara controlled the throne until the reign of Emperor Go-Sanjo (1068-73), the first emperor not born of a Fujiwara mother since the ninth century. Go-Sanjo, determined to restore imperial control through strong personal rule, implemented reforms to curb Fujiwara influence. He also established an office to compile and validate estate records with the aim of reasserting central control. Many shoen were not properly certified, and large landholders, like the Fujiwara, felt threatened with the loss of their lands. Go-Sanjo also established the Incho, or Office of the Cloistered Emperor, which was held by a succession of emperors who abdicated to devote themselves to behind-the-scenes governance, or insei (cloistered government).

The Incho filled the void left by the decline of Fujiwara power. Rather than being banished, the Fujiwara were mostly retained in their old positions of civil dictator and minister of the center while being bypassed in decision making. In time, many of the Fujiwara were replaced, mostly by members of the rising Minamoto family. While the Fujiwara fell into disputes among themselves and formed northern and southern factions, the insei system allowed the paternal line of the imperial family to gain influence over the throne. The period from 1086 to 1156 was the age of supremacy of the Incho and of the rise of the military class throughout the country. Military might rather than civil authority dominated the government.

A struggle for succession in the mid-twelfth century gave the Fujiwara an opportunity to regain their former power. Fujiwara Yorinaga sided with the retired emperor in a violent battle in 1158 against the heir apparent, who was supported by the Taira and Minamoto. In the end, the Fujiwara were destroyed, the old system of government supplanted, and the insei system left powerless as bushi took control of court affairs, marking a turning point in Japanese history. Within a year, the Taira and Minamoto clashed, and a twenty-year period of Taira ascendancy began. The Taira were seduced by court life and ignored problems in the provinces. Finally, Minamoto Yoritomo (1147-99) rose from his headquarters at Kamakura (in the Kanto region, southwest of modern Tokyo) to defeat the Taira, and with them the child emperor they controlled, in the Genpei War (1180-85).

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