In February 1941, Nott was appointed on the staff of the Commander-in-Chief, East Indies Station Admiral Sir Ralph Leatham. The East Indies Station was headquartered at HMS Lanka in Colombo and Nott served as the liaison officer to the C-in-C. In August 1940, Italy invaded British Somaliland annexing it. In early 1941, Operation Appearance was being planned to re-take British Somaliland. Nott played an important part in the arrangements for seaborne supplies for the advancing forces in Italian Somaliland. On 19 April 1941, he was promoted to the acting rank of Commander. For good services in operations off the coast of Italian East Africa, he was mentioned in dispatches on 30 September 1941. He was appointed Staff Officer (Operations) to the Senior Naval Officer, Persian Gulf. He subsequently moved to the Royal Naval base in the Persian Gulf - "HMS Seabelle". For his services in the Persian Gulf, he was mentioned in dispatches for the second time. In September 1941, he moved to Naval headquarters as the Staff Officer (Plans). During this tenure, on 28 May 1942, he was promoted to the substantive rank of commander. He subsequently worked towards dealing with the menace of Japanese submarines in the Arabian Sea.