Islands with a view to reconciling them to British rule, and on his advice the proposed Church of England (Canterbury) settlement, which was at first designed for
the Bay of Islands, was formed instead at Port Cooper on Middle Island, where natives were fewer. At the end of August Clarke returned to Van Diemen's Land to become private secretary to Sir William Denison, the governor. In 1851 he took his seat on the new legislative council, and was put in charge of some government measures.
In May 1853 Clarke moved to Melbourne to become surveyor-general of Victoria, with a seat on the legislative council. Promoted second captain on 17 Feb. 1854, he drafted the bill for a new constitution for the colony, on a representative basis. This was carried in the council early in 1854. At the same time he took a prominent part in organising the Melbourne Exhibition of 1854, and in founding the Royal Philosophical Society of Victoria, of which he was the first president. In the autumn he carried a useful bill (known as Clarke's Act) to enable the inhabitants of any locality, not less than a hundred in number and not spread over a greater area than thirty-six square miles, to institute automatically a municipality for their district with full municipal powers. The new constitution for Victoria, which was proclaimed in November 1855, relieved Clarke of his appointments on the old terms and provided him with a pension of 800l. a year in case he returned to Europe. Remaining in the colony, Clarke stood and was returned for the constituency of South Melbourne, and entered the cabinet of Mr. Haines as surveyor-general and commissioner of lands. In these capacities he was associated with the inauguration of railways in the colony, starting with 185 miles of trunk road in 1857. It was soon arranged that Clarke as head of the land department, with Captain Charles Pasley [q. v.], the chief of the public works department, should become permanent heads of their departments, retiring from the cabinet, but retaining their parliamentary seats. In the session 1857-8 Clarke, always a strong radical, urged universal suffrage in opposition to the premier, and defeated the government. Being refused a dissolution, he declined the governor's invitation to form a new administration.
After promotion to first captain on 19 March 1857, Clarke decided to return to England for military duty. In January 1859 he was accordingly appointed to the command of the royal engineers at Colchester. While there he gave the war office and the government valuable advice on colonial matters. In 1862 he was transferred to the Birmingham command. Towards the end of 1863 he was sent with the local rank of major to the Gold Coast of Africa, where a state of war existed with the King of Ashanti He gave varied assistance, acting temporarily as chief justice. At Lagos, where he suffered seriously from fever, he wrote a valuable report on the Gold Coast. His information proved useful ten years later to Sir Garnet Wolseley's Ashanti punitive expedition, the despatch of which he strongly deprecated.
After serving in London temporarily in 1864 as agent-general of Victoria in place of his former colleague in the Victorian government, Hugh C. E. Childers [q. v. Suppl. I], who now became a lord of the admiralty, Clarke was made in August director of engineering works at the admiralty. He was reappointed for a second term of five years in 1869, when he was awarded the C.B. (civil). In this post he thoroughly proved his efficiency. To meet the needs of the new ironclad fleet and the rapid increase in the size of battleships, he devised large extensions to the docks at Chatham and Portsmouth, and new docks at Queenstown, Keyham, Malta, and Bermuda, at a cost of many millions sterling.
In January 1870 he and the hydrographer of the navy, Captain G. H. Evans, officially visited the new Suez Canal and reported that the carrying capacity of the canal only excluded large ironclads and transports, which with increased width of waterway could readily pass through. Clarke recommended the purchase of the canal by an English company to be formed for the purpose. Promoted regimental lieut.-colonel on 6 July 1867, and full colonel in the army on 6 July 1872, he was created a K.C.M.G. in April 1873.
On leaving the admiralty Clarke became governor of the Straits Settlements. He arrived at Singapore on 4 Nov. 1873, and during his eighteen months' stay there put down piracy, which was rampant on his arrival, made settlements with the native states by which British residents were appointed to advise the rajahs and sultans, placed the secret Chinese societies under effective control, cultivated the friendship of his neighbour the Maharaja of Johore, and visited Chululonkorn, the King of Siam, at his request. His policy made for peace and laid the foundation of the present
