This depends on the place and time, but the general answer would be the secular ruler of the given territory. Only portions of Italy were governed directly by the Church. In all other places, there was a secular ruler of some sort (who might have also been an ecclesiastic, as in the case of some of the German principalities ruled by Prince-Archbishops and the like) and those rulers were responsible for setting up the civil and criminal laws (the Church only had power over cannon law). In some places, depending on the time, there might have also been consultative assemblies to help the executive (such as the Venetian Republic or the Kingdom of England), which carried various degrees of influence and power.