In 970 the Tendai Buddhist
Zasu or Great Abbot Ryogen established a standing army, first to settle a dispute with the Gion Shinto
Shrine and then as a force to be called upon whenever the Tendai schools interests were compromised.
These interests had little to do with doctrinal differences but much to do with the vast land holdings of various monasteries and their other forms of wealth such as scrolls, statuary, and so on.
In 1081 the monastery Kofukuji in Nara joined their forces with other monasteries to attack Mount Hiei and Miidera, the two main Tendai branches, razing the latter and looting both.
By 1100 all of the larger Tendai monasteries and leading Shinto shrines such as those at Gion, Kumano, Kitano, and Hiyoshi all had standing armies.
Between 981 and 1185 Mount Hiei sent thousands of warrior monks (sohei) wearing robes over armour into Heiankyo (Kyoto) to threaten the imperial court. Often the disputes were about land titles or taxation. The imperial court of the Heian era kept no standing army but depended on the forces of various clans. The clan which held the real power in Japan at the time, the Fujiwara, preferred manipulation and diplomacy over violence. As a consequence the court almost always ceded to the demands of the sohei.
Other schools also developed corps of warrior monks, such as the Shingon branch at Negoro in the province of Kii.
The conduct of the Tendai and Shingon schools of the time brought about great dissatisfaction and dissident sects of Buddhism began to form and then erupt in the Kamakura era.
During the Gempei war (1180) the Miidera temple supported the wrong side and was destroyed and Nara was besieged. In all some 3500 monks died in the blaze and the massacre that followed.
A bribe kept Kyoto out of this war. Although the temple was rebuilt, it was not until 200 years later that the monks again became a powerful force in Japan. Even then the monks did not hold their former positions. In this time a new style of fighting emerged, less monastic and more populist then before, spreading to all regions of society and forming the Ikko ikki ("devoted-riot").
Still the largest sect in present day Japan, the Jodo Pure Land sect promised rebirth in paradise to those who died in battle. In 1488 the Ikko rebelled and won control of Kaga province.
From here the sect spread and by 1570 they had established themselves at many key locations, with two main power bases. Well equipped and armed, these armies were not merely a rabble but instead were a major force to contend with, often defeating and nearly driving to seppuku, Tokugawa Ieyasu the future shogun.
After eleven bloody years the Ikko ikki were finally defeated in 1580 by Oda Nobunaga at Ishiyama Hoganji, their fortress monastery. Wave after wave of assaults on the fortress were unsuccessful and after a 4 year siege a peace-treaty was drawn up, ending the conflict, sparing the life of the Ikko ikki leader, Shimotsuma Nakayuki.