This system had various problems, however, including that of pardons granted too frequently; of temples Kanei-ji and Zojo-ji that were supposedly apolitical were allowed to recommend pardons; of recommendations that only the family of a convict were allowed to ask for (thus it was hardly possible for convicts who had no relatives); and of obscure criteria for granting a pardon because the conference chamber discussed the propriety of each case separately.
しかし、恩赦そのものが濫発されたうえ、本来政治とは無関係である寛永寺や増上寺による口添えの存在、しかもその口添えは受刑者の家族しか出来ない事など（独身者には困難である）様々な問題を抱えており、更に個々の受刑者の恩赦の是非は評定所の個別の審議を経たためにその適用基準も曖昧であった。