There are various theories about the issuing of this Expelling edict and the cause could be that Hideyoshi was furious at the residents rejecting his order to bring a woman of Arima because she was Christian, that Coelho, Vice-Provincial of the Society of Jesus in Japan at that time boasted as if the Spanish Armada was under his command in front of Hideyoshi during the expedition to Kyusyu, that the Christian feudal lords such as ARIMA and OMURA in Kyushu destroyed shrines and temples as well as persecuted monks and made huge donations to the churches, and that the Society of Jesus did not obey when he tried to apply the policy to Nagasaki, the domain of the Society, they dissolved the old domains of temples and shrines inherited from Nobunaga ODA and place them under a unified regime, and that some of the missionaries conducted human trafficking (selling the Japanese to outside Japan as slaves).
この追放令が出た背景には諸説あり、秀吉が有馬の女性を連れてくるように命令した際にキリシタンであることを理由に住民が拒否し秀吉が激怒したとも、九州征伐に向かった秀吉の目の前で、当時の日本イエズス会準管区長でもあったコエリョがスペイン艦隊が自分の指揮下にあるごとく誇示した事が原因とも、九州の有馬氏や大村氏などのキリシタン大名が寺社仏閣を破壊すると同時に、僧侶にも迫害を加えたり教会へ莫大な寄進を行っていた事が理由とも、また織田信長から継承した旧来の寺社領を解体して統一政権の支配下におく政策をイエズス会領である長崎にも適用しようとしてイエズス会側が従わなかったとも、宣教師の一部が人身売買（日本人を奴隷商品として国外へ売り払う）を行っていた事が原因とも言われている。