It became increasingly more difficult even for government-certified Shuinsen ships to travel to other countries due to the isolationist policy of the shogunate government; in 1633, the First Seclusion Order, which forbade all ships other that those carrying official letters of the shogunate government to visit or return from other countries, was issued; and in 1935, the Third Seclusion Order, which forbade all Japanese to travel to or return from other countries, was issued, bringing an end to Shuinsen trade.
江戸幕府の鎖国政策の進展により、幕府公認の朱印船の海外渡航すら難しくなり、1633年老中奉書船以外の海外渡航や帰国を禁止する第1次鎖国令が発令され、1635年にはすべての日本人の海外渡航と帰国を禁止する第3次鎖国令が発令されて朱印船貿易は終末を迎えた。