Havelock joined the colonial civil service upon leaving the army, and was sent to the West Indies in 1877 as President of Nevis. In 1878, he was transferred to Saint Lucia as the colony's Administrator, before returning to the Seychelles as Chief Civil Commissioner.
In February 1881, Havelock was assigned his first governorship in Sierra Leone and the West African settlements. In addition, he was appointed British consul to Liberia, and became involved in a major border dispute between Liberia and Great Britain. The area in question was known as the Gallinas territory, an area lying between the Sewa River and the Mano River, and the vague border between Sierra Leone and Liberia had been unsettled for years. On 20 March 1882, Havelock led a flotilla of four British gunboats to the Liberian capital Monrovia, issuing a demand that Liberia cede all territories up to the Mafa River to Great Britain, and pay an indemnity of £8,500 to British merchant traders for injuries inflicted in 1871 by tribes inhabiting the area of the British claim. A treaty was signed, but its ratification was refused by the Liberian Senate, and Havelock and his gunboats returned to Monrovia in September that year, demanding immediate acknowledgement of the British claims, and ratification of the treaty. The senate refused once more, and although Havelock's diplomacy prevented a bloody conflict, British troops from Sierra Leone marched into the disputed territory several months later. Despite the support of the United States, Liberia realised that resisting the British claim was futile, and signed the treaty in London on 22 November 1885. The border was finally settled in 1903 by a mixed commission from both countries.
In 1886, Havelock became Governor of Natal, where he dealt with the annexation of Zululand in 1887, and an unsuccessful rebellion led by Dinuzulu kaCetshwayo in 1888. He returned to England in 1889, and served on the international anti-slavery commission in Brussels.
In March 1890, Havelock was appointed Governor of Ceylon, where his actions included extending the country's railways to Kurunegala and Bandarawela, and abolishing the 'paddy tax', a levy on rice cultivation.
Havelock left Madras in 1901, and was offered the governorships of the Straits Settlements in Malaya and Victoria in Australia, which he declined due to ill health caused by many stressful years in tropical climates. He was then offered the post of Governor of Tasmania, which he accepted in May 1901, arriving in Hobart to be sworn in on 8 November. His health, however, continued to decline and he made the decision to cut short his term as governor to only two-and-a-half years. He notified the premier, William Propsting, of his resignation on 6 January 1904, and left Tasmania on 16 April.
Later life
Havelock returned to England, and retired to Torquay, Devon. On 15 August 1871, Havelock had married Anne Grace, née Norris, who died in early 1908. Havelock himself died at Bath, Somerset less than six months later on 25 June. He was survived by a daughter.