Two years later Lord Justice Drury and Sir Edward Fyton， Treasurer， announced to the privy council that on their arrival in Kilkenny the Protestant Bishop of Ossory reported to them "that not only the chiefest men of that town (as for the most part they are bent to Popery) refused obstinately to come to the church， and that they could by no means be brought to hear the divine service there with their wives and families (as by her Majesty's injunctions they are bound to do)， but that almost all the churches and chapels or chancels within his diocese were utterly ruined and decayed， and that neither the parishioners nor others that are bound to repair them and set them up could by any means be won or induced to do so." The Lord Justice and his companion called the chief men of Kilkenny before them， and bound them in recognisances of ā40 each "that they and their wives should duly every Sunday and holiday frequent the church， and hear the divine service."[95]
Waterford was equally bad. In 1579 Sir William Pelham reported that Marmaduke Middleton， who had been appointed bishop by Elizabeth， had met with a bad reception in Waterford， "partly through the contemptuous and obstinate behaviour of the mayor and his brethren of that city， and partly by the clergy of that church." The Dean of Waterford had made himself particularly disagreeable， and on account of his behaviour Pelham recommended that he ought to be deprived of his dignity as an example to the citizens who were "the most arrogant Papists that live within this state." Bishop Middleton was most anxious to get himself removed from Waterford， where he feared that his life was in danger. He reported that Waterford was given over to "Rome-runners and friars，" that clergy and people were united to prevent her Majesty's most godly proceedings， that "Rome itself held no more superstition" than the city over which he ruled， and that most of the Protestant incumbents were little better than "wood-kerne."[96]
Even towards the end of Elizabeth's reign Waterford was still， as it had been when she ascended the throne， strongly Catholic. The privy council in England warned Sir George Carew that though "the evil disposition of the Irish people in most places of that kingdom， and especially of the inhabitants of Waterford， in matters of religion"was perfectly well known， and though great toleration had been shown them lest they should have an excuse to rise in rebellion， "yet something must be done to repress the presumption and insolency of the people." For it had been announced by the Archbishop of Cashel (Magrath) "that in Waterford there are certain buildings， erected under colour and pretence of almshouses or hospitals， but that the same are in very deed intended and publicly professed to be used for monasteries and such like houses of religion， and that friars and popish priests are openly received and maintained in them . . . and exercise their service of the Mass openly and usually in many places， as if they were in no awe or fear of any exception to be taken thereunto." It is noteworthy， however， as indicating the extent of English influence at that time in Ireland， that the members of the privy council warned the President of Munster that they "do not think it convenient that any extraordinary course should be taken or any disturbance made to inquire after or to punish them for their Masses or any other popish superstitions， unless they show thereby openly to the world an insolent contempt for her Majesty's authority."[97]
In 1597， when Lord Borough was sent over as Lord Deputy， Elizabeth instructed him to discreetly inquire of the state of religion， whereof we are informed，" she wrote， "there hath been notorious negligence， in that the orders of religion are in few parts of our realm there observed； and that which is to be lamented， even in our very English Pale multitudes of parishes are destitute of incumbents and teachers， and in the very great towns of assembly， numbers not only forbear to come to the church or divine service， but [are] even willingly winked at to use all manner of popish ceremonies." She ordered him to examine into the causes of "this general defection，" to see what have the Ecclesiastical Commissioners been doing all these years， and to forward his views as to how "this general defection might be reformed， in some convenient sort， and not thus carelessly suffered as though she had granted toleration of Popery."[98] Three years later (1600)Sir George Carew furnished a very gloomy report on the progress of the new religion. "If the Spaniards do come hither，" he wrote， "I know no part of the kingdom that will hold for the queen， and the cities themselves will revolt with the first. For it is incredible to see how our nation and religion is maligned， and the awful obedience that all the kingdom stands in unto the Romish priests， whose excommunications are of greater terror unto them than any earthly horror whatsoever.
Until of late， although the townsmen have ever been obstinate Papists， yet /pro forma/ the mayors and aldermen would go to the church. But now not so much as the mayors will show any such external obedience， and by that means the queen's sword is a recusant， which in my judgment is intolerable. Nevertheless I do not think it good to insist much upon it in this troublesome time. As for Masses and such slight errants here， they are of no great estimation. I am not over-curious to understand them， so as they be not used contemptuously and publicly in derogation of the queen's laws. But the mayors of the cities and corporate towns to be let run in so manifest contempts I do not wish."[99]