In 1636, Governor Corcuera, like Governor Dasmariñas, complained to the king that the friars were infinitely more powerful than the Crown's representatives. But monastic supremacy was a fact of life the King's representatives had to live with. Those who dared oppose the religious courted humiliation and even death. Governor Diego de Salcedo was imprisoned by the Inquisition and died a broken man while he was being shipped back to Mexico in 1669.
The dispute between Church and State flared up with particular violence during the term of Governor Juan de Vargas in the third quarter of the seventeenth century.
When Vargas was no longer governor, his implacable foe, Archbishop Pardo, forced him to stand each day for four months in Manila's streets wearing sackcloth and with a rope around his neck and a candle in his hand. He, too, died a prisoner on a galleon bound for Mexico.
Governor Fernando Manuel de Bustamante came into conflict with the Church when, after finding out that the friars had borrowed heavily from the government and from the obras pias, he ordered them to return the money. The governor's assertion of his official authority in this and other matters put him on a collision course with the clergy. Their mutual hostility culminated in the arrest and imprisonment of the Archbishop on charges of having conspired against the government. The friars at the head of a mob, forced their way into the governor's palace and stabbed Bustamante to death.