Soon after fatal Flodden, Adam, Earl of Sutherland, in anticipation of threatened dangers in the North, made overtures to Earl John, and entered into bonds of friendship and alliance with him for mutual protection and support. The better to secure the goodwill and assistance of the Earl of Caithness, Earl Adam made a grant of some lands on the east side of the water of Ully; but the Earl of Caithness, although he kept possession of the lands, joined the foes of his ally and friend. [Gordon, an historian of known bias to the House of Sinclair] The Earl of Sutherland had also established a league of amity with Y-Roy-Mackay the same year, but he presently dying, a contest ensued for the succession to Strathnaver between his brother Neil and his two bastard sons John and Donald. John took possession, but Neil laid claim and applied to the Earl of Caithness for assistance to recover them. After many entreaties the Earl put a force under Neil and his two sons, and they promptly dispossessed John, but were surprised by Donald, who slew his cousins, and, being rejoined by John, captured Neil - who, being abandoned by the Earl of Caithness, had cast himself on their generosity and regardless of mercy and the ties of blood, ordered him to be beheaded in their presence by the hands of Claff-na-Gep, his own foster-brother. [From History of the Scottish Clans].
The Earls of Caithness and Sutherland were continually in opposition, and at last the latter brought an action before the Lords of Council and Session to recover the lands of Strathully all the grounds of non-fulfilment of the consideration, viz., to assist the Earl of Sutherland against his enemies. There were other minor points of dispute between the Earls, to get all which determined they both repaired to Edinburgh. Instead, however, of abiding the issue of a trial at law before the judges, both parties, by the advice of mutual friends, referred the decision of all the points in dispute on either side to Gavin Dunbar, Bishop of Aberdeen, who pronounced his award at Edinburgh on the 11th March 1524, his judgment appearing to have satisfied both parties, as the Earls lived in peace with one another ever after".
In 1528 he was one amongst others to whom King James addressed a mandate urging the extirpation of the "Kin of Clan Chattan"; but nothing severe seems to have been done to that then troublesome clan; The letter reads " to our louittis cousins Adam Earl of Sutherland; John Earl of Caithness," etc. [From History of the Scottish Clans].
Earl John's next appearance is his last.
Under 1528 Tytler, quoting Lesley, has:
There now ensued a formidable but abortive attempt to separate the Orkneys from the dominion of the Crown. The author of the rebellion, whose ambition soured to the height of an independent prince, was the Earl of Caithness; but his career was brief and unfortunate: the majority of the islanders were steady in their loyalty and in a battle James Sinclair, the Governor of Orkney, encountered the insurgents, defeated and slew their leader with five hundred men, and making captives of the rest, reduced these remote parts to a state of peace.
The Groat Inventories contain a Precept of Sasine by John Sinclair, Earl of Caithness, for infefting John Groat in one penny land in Duncansbay. Dated at Noss, 5th October 1515. The Sasine thereanent, issues on 12th October following, and another of even date to William Groat in a farthing land, also in Duncansbay. On the 28th September, 1521, a Precept of Sasine issues from Earl John for infefting Walter, son and heir of umquhile [deceased] William Groat in the said lands; and he dates another at Girnigoe, 22nd October 1523, infefting John Groat in one penny land in Duncansbay conform to a charter granted yr. anent. [Petrie Papers] Earl John granted to Alexander Brisbane of Reiss a charter of Ekirnoss, dated Girnigoe Castle, 25th March 1520; [Bruce - Caithness MS] and there is another dated Wick, 19th October 1523, one of donation to Trinity Convent, Aberdeen, for the soul of his father, of himself, and the souls of his friends and successors, 264 masses to be sung yearly in all. [Bains Merchant Guilds of Aberdeen]
By his Countess Elizabeth, daughter of Sir William Sutherland of Duffus, he had
He had also a natural son -
DAVID, Bailie to the Bishop of Caithness. In 1556 Earl George obtained a remission for imprisoning David in Girnigoe Castle. [Henderson].
Some authorities state that Earl John married secondly, after the death or divorce of Elizabeth Sutherland, the fifth sister of Adam Gordon, Earl of Sutherland, but this seems exceedingly doubtful. It arises perhaps from confusing Sir William Sinclair of Warsetter, Orkney, who married Helene, fifth daughter of George, Earl of Huntly, with his contemporary and kinsman, the Earl of Caithness.