There were examples in which sects like Nichiren shu Fujufuse ha (Nichiren sect's Not Receive and Not Give School) were persecuted as they were considered to be a heresy, or in which Jodo Shinshu was banned in certain domains (See Kakure Nenbutsu).
なお、日蓮宗不受不施派のように幕府から邪宗門として迫害された宗派や特定の藩において浄土真宗が禁じられた例（隠れ念仏を参照のこと）もある。