The appeal of these Catholic lords, backed[8] as it was by the danger of a new and more general rebellion, was not without its effects in England. In January 1607 the privy council in England wrote to Sir Arthur Chichester, Lord Deputy, that although "the reformation of the people of Ireland, extremely addicted to Popish superstition by the instigation of the seminary priests and Jesuits, is greatly to be wished and by all means endeavoured, still, a temperate course ought to be preserved." There should be no question of granting toleration, but at the same time there should be no "startling of the multitude by any general or rigorous compulsion." The principal men in the cities who show themselves to be the greatest offenders should be punished; the priests and friars should be banished, but no "curious or particular search" should be made for them; Viscount Gormanston and his companions should be released under recognisances, except Sir Patrick Barnewall who was to be sent into England; the Dublin aldermen should be treated in a similar manner but should be obliged to pay the fines, and the Protestant clergy should be exhorted to take special pains to plant the new religion "where the people have been least civil."[9]

But Chichester, Davies, Brouncker, and their companions had no intention of listening to the counsels of moderation. They continued to indict the poorer classes according to the clauses of the Act of Uniformity and to cite the wealthier citizens before the Star Chamber for disobedience to the royal mandates.[10] In Waterford Sir John Davies reported "we proceeded against the principal aldermen by way of censure at the council table of the province for their several contempts against the king's proclamations and the special commandments of the Lord President under the council seal of Munster. Against the multitude we proceeded by way of indictment upon the Statute of 2 Elizabeth, which giveth only twelve pence for absence from church every Sunday and holiday. The fines imposed at the table were not heavy, being upon some £50 apiece, upon others £40, so that the total sum came but to £400; but there were so many of the commoners indicted that the penalty given by the statute (twelve pence) came to £240 or thereabouts."[11] Punishments of a similar kind were inflicted in New Ross, Wexford, Clonmel, Cashel, Youghal, Limerick, Cork, and in all the smaller towns throughout Munster. In Cork the mayor was fined £100, and in Limerick more than two hundred of the burgesses were indicted, the fines paid by these being given for the repair of the cathedral.[12] Steps were also taken in Connaught to enforce attendance at the Protestant service. Five of the principal citizens of Galway were summoned before the court and fined in sums varying from £40 to £20, and punishments of a lesser kind were inflicted in other portions of the province. In Drogheda "the greatest number of the householders together with their wives, children, and servants," were summoned and fined for non-attendance at church. In Meath, Westmeath, Longford, King's County, and Queen's County the government officials were particularly busy.

But though here and there a few of the prominent citizens and of the poorer classes were driven into public conformity by fear of punishment, the work of winning over the people to Protestantism made little progress. In Cashel the Commissioners reported (1606) that they found only one inhabitant who came to church, and even "the Archbishop's (Magrath) own sons and sons-in-law dwelling there" were noted as obstinate recusants."[13] Brouncker, President of Munster, was particularly severe in his repressive measures, so much so that on his death (1606) his successors were able to announce "that almost all the men of the towns are either prisoners or upon bonds and other contempts," but they added the further information that many of those who had been conformable in his time had again relapsed. The Protestant Bishop of Cork complained (1607) that in Cork, Kinsale, Youghal, and in all the country over which he had charge no marriages, christenings, etc., were done except by Popish priests for seven years, that the country was over-run by friars and priests who are called Fathers, that every gentleman and lord of the country had his chaplains, that "massing is in every place, idolatry is publicly maintained, God's word and his truth is trodden down under foot, despised, railed at, and contemned of all, the ministers not esteemed - no not with them that should reverence and countenance them." "The professors of the gospel," he added, "may learn of these idolators to regard their pastors."[14] Sir John Davies with his usual keen insight placed the blame for the comparative failure of the Protestant clergy. "If our bishops, and others that have care of souls," he wrote (1606), "were but half as diligent in their several charges as these men [the Jesuits and seminary priests] are in the places where they haunt, the people would not receive and nourish them as now they do. But it is the extreme negligence and remissness of our clergy here which was first the cause of the general desertion and apostasy, and is now again the impediment of reformation."[15] The Catholics had protested continually against the proceedings under royal mandates as illegal, and their protests were brought before the English privy council by Sir Patrick Barnewall, who had been sent over to London as a prisoner. The judges in England condemned the proceedings in Ireland as unwarrantable and without precedent. Barnewall was allowed to return to Ireland in 1607, and the new method of beggaring or Protestantising the wealthier class of Irish Catholics was dropped for the time.