Ninnis spent the remainder of his career working on ships and in hospitals. His surgical notes from at least part of this time survive; in November 1880, for example, while serving aboard HMS "Garnet", he recorded a failed attempt to revive a drowning victim, James Farley: "Brandy injected into the rectum and strychnine at the epigastrium area immediately below the heart, brandy and ammonia to wet his mouth." In 1879 he was awarded Sir Gilbert Blane's gold medal, an honour reserved for Royal Navy medical officers. In 1883 he received his final active promotion, to Deputy Inspector-General. He was appointed Principal Medical Officer at Melville Naval Hospital, Chatham in 1892, and three years later was selected as a Knight of Grace to the Venerable Order of Saint John. He retired on 1 September 1897, with an honorary promotion to Inspector-General.