Ommanney was promoted commander on 9 October 1840, and from August 1841 to the end of 1844 served on board the steam sloop HMS "Vesuvius" in the Mediterranean Sea. Here he was employed on the coast of Morocco for the protection of British subjects during the French hostilities, which included the bombardment of Tangier by the Prince de Joinville's naval squadron. Ommanney was promoted captain on 9 November 1846, and from 1847 to 1848 was employed under the government commission during the Irish Famine, carrying into effect relief measures and the new poor law. In 1845 Ommanney was elected a Fellow of the Royal Geographical Society, and on 4 June 1848 he was elected a Fellow of the Royal Society (FRS).