In his later career Ninnis served both on ships and in hospitals. He received Sir Gilbert Blane's gold medal in 1879, was promoted to Deputy Inspector-General in 1883, was appointed Principal Medical Officer at Melville Naval Hospital in 1892, and was selected as a Knight of Grace of the Venerable Order of Saint John in 1895. Upon his retirement in 1897 he was promoted to Inspector-General, and in 1900 and 1902 served as President of the Section of the Navy, Army, and Ambulance of the British Medical Association. He was made a Commander of the Royal Victorian Order (CVO) in 1912. Ninnis was initiated into the Freemasons 1872, was a founder of several Lodges, and in 1901 became a Past Grand Deacon of England. He was the father of Belgrave Edward Sutton Ninnis, an explorer who was lost down a crevasse during the 1911–14 Australasian Antarctic Expedition.