In the early Edo period, the temple fell under the control of the Shogunate and the former chief priest Takuan Soho was forced into exile in what is known as The Purple Robe Incident, but relations with the Shoganate subsequently recovered.
江戸時代初期に幕府の統制を受け、紫衣事件と呼ばれる元住持・沢庵宗彭が流罪となる圧迫を受けたが、幕府との関係ものちに回復した。