John Hunter faced three major problems in running the colony.  First, there was a division of responsibility between different institutions in London. As governor, Hunter was responsible to the King through the Duke of Portland, Secretary of State for the Home Office. Since NSW had no means to express public opinion, Portland was influenced by private correspondence from discontented residents such as Macarthur and the governor was rarely aware of the entire information at the disposal of the government when it made its decisions. Although the Home Office was responsible for the convicts and the colony, it had to rely on the Admiralty for transport to convey prisoners to Sydney Cove. The military were the responsibility of the Secretary at War and the commissariat and the Ordnance Department was responsible for military buildings. The Treasury, the Mint and two audit officers were concerned with the financial interests of the colony and the Post Office had the relatively easy task of dispatching mail whenever opportunity arose. Secondly, within NSW itself, the relationship between the civil and military establishments had been problematic since 1788 and the establishment of the New South Wales Corps and the decision by Grose to grant them land and their monopolistic attitude to the spirit trade made existing tensions even more difficult.
Every day convinces me more and more that many of those people, if they cannot be prevail’d on to make their public office their first consideration, shou’d be remov’d. Their private concerns occupy all their time, and £50 per annum seems to be no object when £300, £400, or £500 is to be gained by trade.
There were also the beginnings of the division between convicts, emancipists (convicts freed on a variety of conditions) and free settlers and between public and private sectors. Finally, the outbreak of war with France in 1793 had exacerbated this situation calling into question excessive government spending in NSW and, although the colony was not forgotten, it inevitably was not viewed as important a priority as had been the case before 1793. The potential for tensions between these different elements had existed from the founding of the colony but grew in significance from the mid-1790s when the survival of the colony was assured and food shortages became less common. Even so, Hunter complained in his first letter of Portland of the scarcity of salt and that the colony was ‘destitute of every kind of tool used in agriculture’. As late as September 1798, Hunter was concerned that the people were ‘literally speaking, nearly naked and a great number without a bed or blanket to lie upon’.
Hunter’s first impressions on his return to NSW, as recorded in his official dispatches, were favourable, but as he privately confessed later in a letter to Sir Samuel Bentham that he had little understanding of the nature of his ‘irksome command’ when he solicited the appointment. By October 1795, he had become aware of the enormity of his task commenting to Portland on the extent to which the settlement had expanded and the problems this had created for effectively maintaining its security and administration. This is reflected in the flurry of government and general orders he issued in the remainder of 1795 including one preventing the indiscriminate felling of timber on the Hawkesbury. Hunter had a resident civil establishment of thirty-one including medical staff and superintendents of convicts, master carpenters and the like, but less than a third could be considered serious official advisers. The number of officers on duty with the NSW Corps was seventeen. There was considerable difference in age between the newly arrived governor, approaching 60 and those who might be called on to act as his advisers. Macarthur, as inspector of public works on whom Hunter relied in the early months of his governorship until the Baughan affair, was 28. Captain Paterson, the Corps commandant was 40; Captain Joseph Foveaux was 30; almost everyone else was younger than Paterson. Hunter as an experienced officer was accustomed to naval discipline and expected to see it reflected in NSW. Instead, he faced an entrenched military force and an increasingly dispersed body of settlers largely dependent at the mercy of the monopolistic trading practices of the military hierarchy and other officials. His instructions would have been difficult to implement even if he had a loyal and competent public service with reliable military support.
 Hoyle, Arthur, The Life of John Hunter, Navigator, Governor, Admiral, (Mulini Press), 2001, Auchmuty, J.J., ‘Hunter, John (1737-1821)’, ADB, Vol. 1, pp. 566-572. See also, Wood, G.A., ‘Governor Hunter’, Journal and Proceedings (Royal Australian Historical Society), Vol. 14, (6), (1928), pp. 344-362. For Hunter’s commission and instructions, see HRNSW, Vol. 2, pp. 110-117, 227-234 and HRA, Series I, Vol. 1, pp. 513-527.
 William Henry Cavendish-Bentinck, 3rd Duke of Portland (1738-1809) was a Whig politician for the first thirty years of his political career but as a conservative Whig, Portland was deeply uncomfortable with the French Revolution, and ultimately broke with Fox over this issue, joining Pitt’s government as Home Secretary in 1794, a position he held until 1801. Briefly an MP, Portland succeeded to the title in 1762 but did not make his maiden speech in the House of Lords until 1783; one of his claims to fame is that he rarely spoke in parliament. See, Wilkinson, David, The Duke of Portland: politics and party in the age of George III, (Palgrave), 2003, pp. 108-136 for his period at the Home Office.
 Hunter expressed his concern about Macarthur in a letter to Portland on 14 September 1796, HRNSW, Vol. 3, pp. 129-131 in which he made clear that ‘...this officer’s conduct...[was] impertinent, indirect and highly censurable interference in the dutys and department of the Governor of this colony...’
 The problem of spirits concerned Hunter from the outset. His general order of 23 January 1796 prohibited the making of spirits in the colony: HRNSW, Vol. 3, p. 10; general order 11 July 1796 took action over the unlimited sale of spirits, HRNSW, Vol. 3, pp. 58-59; general order 12 December 1796, HRNSW, Vol. 3, pp. 185-186 on the link between crime and spirits;
 Hunter to Portland, 20 June 1797, HRA, Series I, Vol. 2, p. 22.
 Hunter to Portland, 11 September 1795, HRNSW, Vol. 2, p. 318.
 Hunter to Portland, 25 September 1798, HRNSW, Vol. 3, p. 493.
 Hunter to Portland, 11 September 1795, HRNSW, Vol. 2, pp. 318-319 stated that ‘agriculture...far exceeds any expectation...and does great credit to the arrangements made by...Grose and...Paterson’.
 Hunter to Bentham, 20 May 1799, HRNSW, Vol. 3, pp. 673-675.
 Hunter to Portland 25 October 1795, HRNSW, Vol. 2, pp. 328-329.
 Hunter to King, 5 December 1795, HRNSW, Vol. 2, p. 341.
 The civil establishment is listed in HRNSW, Vol. 2, pp. 331-332.
 They are listed in HRNSW, Vol. 2, p. 330.
 Initially Hunter retained the services of Macarthur see, Hunter to Portland, 25 October 1795, HRNSW, Vol. 2, p. 327 but their relationship quickly deteriorated into acrimony, see correspondence between Macarthur and Hunter between 24 and 29 February 1796 printed in HRNSW, Vol. 3, pp. 26-29 that resulted in Macarthur’s resignation as inspector of public works. Macarthur became increasingly critical of Hunter’s administration, see, Macarthur to Portland, 15 September 1796, HRA, Series I, Vol. 2, pp. 89-93.
 Fletcher, B.H., ‘Foveaux, Joseph (1767-1846)’, ADB, Vol. 1, pp. 407-409. Promoted to major in 1796, as senior officer in the absence of Lieutenant-Colonel William Paterson between August 1796 and November 1799 he controlled the NSW Corps during a period when some of its officers were making their fortunes from trading and extending their landed properties. Whether Foveaux was a trader is unknown but he certainly turned his hand to stock-raising. By 1800, he had 1,027 sheep on the 2,020 acres of land he had been granted, making him the largest landholder and stock-owner in the colony. See also, Whitaker, Ann-Maree, Joseph Foveaux: power and patronage in early New South Wales, (University of New South Wales Press), 2000.
 For Hunter’s instructions, see HRNSW, Vol. 2, pp. 227-234.