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As a young man he wished to obtain an official post in Uganda where his friend Major Thruston held a senior military appointment. Major Thruston was killed by the mutineers in the revolt of the Sudanese troops in Uganda in 1898, and it was perhaps fortunate for Duff that the Foreign Office offered him in 1897 the post of an Assistant Resident in the British Central Africa Protectorate, as he might otherwise have shared his friend’s fate. He accepted the offer and proceeded direct from India, where he was travelling at the time, to the Protectorate.
With the appointment of Mr. (later Sir Alfred) Sharpe in 1897 as the new Commissioner the country may be said to have embarked upon the normal course of a settled British dependency with a future before it of steady, if not sensational progress. In this new era of development Duff and his colleagues in the provincial administration were called upon to play an important part. To them was entrusted the duty of maintaining peace among the natives by peaceful methods, of assisting them in the agricultural development of their lands, and so forth.
In 1903 Duff resigned but was re-appointed in the early part of the following year. In 1906 he was promoted to be Resident and in 1911 he was further promoted to a First Grade Residentship. From this time onwards he frequently acted as Deputy Governor. The control of the Protectorate had been transferred from the Foreign Office to the Colonial Office in 1904 and the post of Consul-General had been abolished. By an Order in Council which came into force in October, 1907, the Commissioner became a Governor and Commander-in-Chief and Executive and Legislative Councils were established. Also the old name of the “Nyasaland Protectorate” was revived.