When the shoen system collapsed in the disturbances during the Nanbokucho period (North and South Dynasties period) and the Sengoku period (Warring states period), many of the jisharyo were lost -- In the Toyotomi administration, kenchi (cadastral surveys) was strengthened, whereby merely a part of shuinchi (estates of temple and shrine confirmed by the shogun and exempted from tax) was protected under the bakuhan system (power structure of bakufu and daimyo domains).
やがて、南北朝時代(日本)や戦国時代(日本)の戦乱によって荘園制が崩壊すると、多くの寺社領が失われ、統一政権では検地の強化によって、一部の朱印地が幕藩体制によって保護されるに過ぎなくなる。