In the financial crisis which occurred at the outbreak of the French war, Sinclair's advice and support were of great assistance to the government. It was he who proposed the formation of a select committee on commercial credit and the issue of exchequer bills to the amount of 5,000,000l. Partly in consequence of this Pitt acceded to Sinclair's request, which he had previously refused, for the establishment of a board of agriculture. The idea of a board did not originate with Sir John (Young, Annals of Agriculture, 1793, xxi. 129; Somerville, System followed by the Board of Agriculture, p. 3); but to him belongs the credit of having by his importunity forced the question on the government. The scheme was carried through parliament, in spite of the opposition of Lord Hawkesbury, Sheridan, Grey, and Fox, who even suggested, as Marshall (Review of Agric. Reports, Introd. p. 23) did later, that the establishment of the board was a ‘job’ organised to put more patronage into the hands of the government. On 23 Aug. 1793 the board's charter was sealed, and Sinclair was appointed president. He at once attempted an account of England by parishes, on the plan of his ‘Statistical Account of Scotland.’ But this was abandoned, largely owing to the opposition of Archbishop Moore of Canterbury. The system substituted was that of county reports for the whole of Great Britain, a rough draft being first printed for distribution among the most intelligent inhabitants of the county, from whose corrected copies the final report was to be compiled. Such an arrangement was of course expensive. Arthur Young [q. v.], who had been appointed secretary of the board by the charter, is said in the ‘Memoirs of Sir John Sinclair’ (ii. 65) to have expressed himself in admiring terms at Sinclair's ‘courage’ in undertaking so ‘stupendous an experiment’ with the small sums at the disposal of the board. Privately Young complained of the president's ‘sole object of incessant printing,’ and described himself as ‘mortified to the quick’ at the publication of such a ‘wretched mass of erroneous and insufficient information’ (Memorandum of 1806, quoted in Journal of Roy. Agric. Soc. 1897, p. 6).
In 1794 Sinclair, at the request of Pitt, raised a regiment of fencibles, six hundred strong, called the ‘Rothesay and Caithness fencibles,’ of which he was appointed colonel. Subsequently he raised another regiment of a thousand men, called the ‘Caithness highlanders,’ for service in Ireland. In 1796 he suggested to Pitt the idea of a loyalty loan. But their relations subsequently became strained once more. Their point of difference is summed up in ‘Public Characters,’ apparently without any ironical intent, as being that Sinclair found ‘that Mr. Pitt valued his simple assent more than his advice’ (i. 47). Sir John was anxious for peace, and officiously corresponded on the subject with Barthelemy. He opposed Pitt in the house on the question, and in February 1798 attacked the ministry in two pamphlets, ‘Letters on the State of the Nation’ and ‘Hints on the Present Alarming Crisis,’ 1798. Whether in consequence of this, or because he considered that Sinclair was not making the best use of the money of the board of agriculture, Pitt, at the annual election of the president in 1798, set up Lord Somerville [see Somerville, John Southey] in opposition to him. According to a familiar anecdote, Sinclair represented to Pitt that the president ought to be a peer. Pitt assented, and nominated Lord Somerville. Somerville was supported by the official members, and gained the presidency by a majority of one, thirteen votes being recorded for Somerville and twelve for Sinclair. Many letters of sympathy and indignation reached Sinclair from (among others) Archbishop Markham, Warren Hastings, the Marquis of Lansdowne, and the Duke of Clarence. But Sinclair's colossal schemes had seriously embarrassed the board during the five years of his presidency, and he left it considerably in debt. In 1806 he resumed the office of president, which he held till 1813.
In 1810 Sinclair was appointed a member of the privy council. He subsequently published extracts from the congratulatory letters of many men of repute, including Dr. Adam Smith, William Wilberforce, the Duke of Northumberland, Arthur Young, and Sir Humphry Davy, ‘explanatory,’ he says, ‘of the feelings of the public on that occasion.’ That this feeling, however, was not universal is shown by two articles in the ‘Quarterly’ (vol. iv. 1810, p. 518; vol. v. 1811, p. 120), in which Sir John and his new honours were mercilessly ridiculed. The immediate cause of this attack was the publication by Sir John of two papers on the then burning question of the respective advantages of bullion and paper money, entitled ‘Observations on the Report of the Bullion Committee’ and ‘Remarks on a Pamphlet entitled “The Question concerning the Depreciation of our Currency,”’ 1810 (cf. Alison, Europe, ix. 645).
A few months later Sinclair was appointed to the post of commissioner of excise, a sinecure of considerable value, although the salary was reduced from the 6,000l. which had been