Fendall returned to
Calcutta in 1815 and was informed he had been appointed
Lieutenant-Governor of Java, an island the British acquired following the
Invasion of Java in 1811. On 12 March 1816 by the last advice from
Batavia, John relieved a sickly Sir
Stamford Raffles as Lieutenant-Governor of
Java, an island which is now a part of the Republic of
Indonesia. Upon his arrival, Fendall was faced with significant administrative arrears and a treasury that was almost depleted, challenges he began to address immediately. Fendall ensured that the ailing Raffles continued to receive the courtesies due to the position of Lieutenant-Governor. The British proceeded to restore sovereignty of the territory to the Sultan in November 1816. In January 1817, the Sultan signed a separate contract with the Netherlands, affording the Dutch sovereignty over Banjarmasin.
Cessation of British rule in Java In 1816, the Dutch sent a fleet to reclaim possession of
Java. However, Fendall had not received orders from the Governor-General, and therefore, stoutly refused to give up possession, and the Dutch had to wait until the orders came. On 19 August, of the same year, the Dutch resumed possession, thus making Fendall the last British Lieutenant-Governor of the island. Fendall left
Java in June 1818, on the ship
Caesar, with the Dutch according him all honours on departure. ==Later career, dispute, and Supreme Council appointment==