The Code of Canon Law stipulates that clerics are forbidden to assume duties that entail participation in the exercise of civil power.
The bishops' conference is requiring around 8,000 Catholic bishops, priests and monks in Japan not to comply with subpoenas to serve as citizen judges even if their action results in a fine, according to the officials.
"We expect our clerics to fulfill their religious obligations by refraining from public duties associated with secular authorities," an organization official said.
Some 450,000 church members are to be allowed to decide whether to serve as lay judges based on their conscience, with the bishops' conference supporting them if on religious grounds they choose not to serve in cases where a death sentence may be handed down.
In the lay judge system that started last month, six citizen judges join three professional judges in examining serious criminal cases, such as murder, and deciding upon sentencing.