Although the practice was once again discontinued in later years, it re-emerged when Shogun Ietsuna TOKUGAWA issued on April 5, 1664 (based on the older calendar), the Kanbun Shuinjo (a vermillion seal letter) to all daimyos (Kanbun no Shuin Aratame), requiring all lords to organize inquisitions for suppressing Christianity in the same year.
その後、再びこの制は途絶えていたが、徳川家綱の代に入った寛文4年4月5日(旧暦)に全ての大名に対して寛文朱印状が交付され（寛文朱印改）、同年に宗門改が全ての領主に対して義務付けられた。