He continued to be active after his retirement from the Navy, twice serving—in 1900 and 1902—as President of the Section of the Navy, Army, and Ambulance of the British Medical Association. In July 1900, serving in this capacity, he delivered an introductory address at the annual meeting of the association. In the address, while arguing that light and fresh air were important for the treatment of wounded sailors, noted that they could "only be obtained in sufficient quantity above the water-line, and to place the sick quarters above the water-line, amidst the hurly-burly of a sea fight, traversed by projectiles and wrecked by exploding shells, is of course out of the question, even supposing that sufficient space could be spared." Instead, he argued for dedicated hospital ships, which "during an action ... would keep out of range but sufficiently close to collect the wounded when the fight was over, and sailing under the regulations of the Geneva Convention would be free from molestation or capture." A related article by Ninnis, "The Treatment of Wounded at Sea", was published in the "Philadelphia Medical Journal" in August 1900, and he expanded on the idea of hospital ships in a 1905 paper to the British Medical Association.