The official correspondence of 1673-9, although it reveals a grievous laxity of discipline[263], exhibits Pepys himself in a favourable light. He had a high sense of the honour of the service, and shewed himself both firm and humane in his dealings with his official inferiors. He was at great pains to keep himself informed of the proceedings of the commanders, and when breaches of discipline were reported to him, he took infinite trouble to arrive at the facts. His admonitions to the offenders, though sometimes a little unctuous, are as a rule in the best Pepysian style.

The decay of discipline in the Restoration period has been associated by some writers with the practice of appointing 'gentlemen captains' without experience to important commands at sea. The matter is discussed by Macaulay, picturesquely but with exaggeration[264]; Pepys, in the Diary, quotes Coventry as referring to the 'unruliness' of the 'young gentlemen captains'[265] and confessing 'that the more of the cavaliers are put in, the less of discipline hath followed in the fleet'[266]; and a Restoration paper printed in Charnock's Marine Architecture[267] very much shocks that author by its 'illiberal and improper observations' on the subject. He admits, however, that 'there certainly appears much truth and solidity in the general principle of them,' though 'it might have been wished for the sake of decency and propriety' that the writer 'had conveyed his animadversions in somewhat less vulgar terms.' The victim of Charnock's criticism traces every kind of evil to the year 1660, when 'gentlemen came to command in the navy.' These 'have had the honour to bring drinking, gaming, whoring, swearing, and all impiety into the navy, and banish all order and sobriety out of their ships'; they have cast their ships away for want of seamanship[268]; they have habitually delayed in port when they should have been at sea; a gentleman captain will bring 'near twenty landmen into the ship as his footmen, tailor, barber, fiddlers, decayed kindred, volunteer gentlemen or acquaintance, as companions,' and these 'are of Bishop Williams's opinion, that Providence made man to live ashore, and it is necessity that drives him to sea.' The writer concludes that 'the Crown will at all times be better able to secure trade, prevent the growth of the naval strength of our enemy, with £100,000 under a natural sea admiralty and seamen captains ... than with three times that sum under land admirals and gentlemen captains not bred tarpaulins.'

With some qualifications this is the view of Pepys. He disclaims hostility to gentlemen captains as such; but he quotes from a speech delivered by Colonel Birch in the House of Commons, in which he had urged that one of the 'present miscarriages' of the navy is that 'employment and favour are now bestowed wholly upon gentlemen, to the great discouragement of tarpaulins of Wapping and Blackwall, from whence ... the good commanders of old were all used to be chosen.'[269] Pepys also refers to the liberty taken by gentlemen commanders of 'thinking themselves above the necessity of obeying orders, and conforming themselves to the rules and discipline of the Navy, in reliance upon the protection secured to them therein through the quality of their friends at Court.'[270] Pepys himself was probably an impartial witness, for he was denounced by each side for favouring the other[271].

It is in a way remarkable that during the period of complaints against gentlemen captains we come upon the first establishment of an examination for lieutenants. Towards the end of 1677 complaints reached the Admiralty from Sir John Narbrough, commanding in the Mediterranean, of the 'defectiveness' of his lieutenants 'in their seamanship.'[272] Pepys also refers to 'the general ignorance and dulness of our lieutenants of ships' as 'a great evil' of which 'all sober commanders at this day' complain. They are 'for the most part (at least those of later standing) made out of volunteers, who having passed some time superficially at sea, and being related to families of interest at Court, do obtain lieutenancies before they are fitted for it.'[273] The result was the adoption on 18 December of a regular establishment[274], drawn up by Pepys[275], 'for ascertaining the duty of a sea-lieutenant, and for examining persons pretending to that office.' A lieutenant was required to have served three years actually at sea; to be 20 years of age at least; to produce 'good certificates' from the commanders under whom he had served of his 'sobriety, diligence, obedience to order,' and 'application to the study and practice of the art of navigation,' as well as three further certificates—from a member of the Navy Board who had served as a commander, from a flag officer, and from a commander of a first or second rate—'upon a solemn examination,' held at the Navy Office, of 'his ability to judge of and perform the duty of an able seaman and midshipman, and his having attained to a sufficient degree of knowledge in the theory of navigation capacitating him thereto.' Candidates were sometimes ploughed[276], and this, as Pepys points out, was an encouragement to the 'true-bred seaman' and greatly to the benefit of the King's service. 'I thank God,' he writes in 1678[277], 'we have not half the throng of those of the bastard breed pressing for employments which we heretofore used to be troubled with, they being conscious of their inability to pass this examination, and know it to be to no purpose now to solicit for employments till they have done it.'

To about the same time as the examination for lieutenants belongs another minor reform—an establishment for the better provision of naval chaplains. In April or May, 1677, the King and Lords of the Admiralty resolved 'that no persons shall be entertained as chaplains on board his Majesty's ships but such as shall be approved of by the Lord Bishop of London.'[278] The proposal originated in the first instance with Pepys, who designed it to remedy 'the ill-effects of the looseness wherein that matter lay, with respect both to the honour of God Almighty and the preservation of sobriety and good discipline in his Majesty's fleet.'[279] The details of the scheme were more fully worked out by resolutions adopted by the Admiralty Commission on 15 December, 1677[280].

An important measure which had an indirect bearing upon discipline was James II's 'establishment about plate carriage and allowance for captains' tables,'[281] dated 15 July, 1686. The title of the establishment gives little indication of its real scope; it was designed to give the Admiralty a better control over ships on foreign service, and at the same time so to improve the position of the commanders as to put them beyond the reach of temptations to neglect their public duty for private gain. The preamble refers to the 'general disorder' into which the discipline of the navy has 'of late years' fallen, and especially to the particular evil arising from 'the liberty taken by commanders of our ships (upon all opportunities of private profit) of converting the service of our said ships to their own use, and the total neglect of the public ends for which they, at our great charge, are set forth and maintained, namely, the annoying of our enemies, the protecting the estates of our trading subjects, and the support of our honour with foreign princes.' Commanders are accordingly forbidden to convey money, jewels, merchandise, or passengers without the King's warrant; and copies of orders given by admirals or commanders-in-chief are to be sent to the Secretary of the Admiralty, as also interim reports of proceedings, and a complete journal at the end of the voyage. In consideration of these requirements, commanders are to receive substantial additional allowances 'for the support of their tables,' ranging from £83 a year to £250 according to the ship's rate.

The reign of James II was in a peculiar degree a period of the framing and revising of 'establishments,' and on 13 April, 1686, a new establishment was made concerning 'volunteers and midshipmen extraordinary.'[282] This appears to be a confirmation of an earlier establishment of 4 May, 1676, designed to afford encouragement 'to families of better quality ... to breed up their younger sons to the art and practice of navigation' by 'the bearing several young gentlemen, to the ends aforesaid' on board the King's ships as 'volunteers,' and to provide employment for ex-commanders or lieutenants by carrying them as 'midshipmen extraordinary' over and above the ordinary complement assigned to the ship in which they sailed. Another 'establishment' of the same period is that of November, 1686, for boatswains' and carpenters' sea stores[283].

During the earlier part of Pepys's second Secretaryship, drunkenness gave a good deal of trouble. For instance, in 1685 the commander of the Diamond complained that his officers were 'sottish, and unfit to serve the King,' particularly the gunner, who was 'dead drunk in his cabin when the powder was to be taken out.'[284] Pepys refers on 5 August, 1684, to 'the generality of that vice, now running through the whole navy,'[285] and on 4 February, 1685, he writes, 'Till that vice be cured, which I find too far spread in the navy, both by sea and land, I do despair of ever seeing his Majesty's service therein to thrive, and as I have given one or two instances of my care therein already, so shall I not fail by the grace of God to persevere in it, as far as I am able, till it be thoroughly cured, let it light where it will.'[286] In these efforts the Secretary of the Admiralty, was soon to be powerfully supported by the new King, 'there being no one vice,' Pepys writes on 15 February, 1685, 'which can give more just occasion of offence to his Majesty than that of drunkenness, for the restraining which, as well in the navy as in every other part of the service, I well know he has immoveably determined to have the severest means used, nor shall I in my station fail (according to his commands and my duty) to give my helping hand thereto.'[287]

In connexion with discipline it may be mentioned that even as early as the Restoration there were labour troubles in the dockyards. In 1663 a separate room was applied for in the new storehouse at Portsmouth for use as a workroom, 'as seamen and carpenters will never agree to work together.'[288] In the same year the clerk of the Portsmouth ropeyard complained of the workmen employed there. By hasty spinning they finished what they called a day's work by dinner-time, and then refused to work again till four o'clock. 'Yesterday,' he writes, 'about twenty-five of them left the work to go to the alehouse, where, I think, they remain.'[289] On 26 March, 1664, the shipwrights and caulkers at Deptford are complained of because they work very slowly, and 'give ill language' when pressed to work[290]. Later on, in January, 1671, Commissioner John Cox appears to have had almost as much trouble with the master workmen and their instruments in Chatham dockyard. They were remiss in their attendance, and met his efforts at their amendment by passive resistance[291].