In 1902 he was deputed to investigate the prevalence of malaria at the Customs stations along the frontier of Goa, and to devise means for removing the position of the Salt Peons who were affected by malaria in these places. During this expedition he discovered a new species of anopheline mosquito, which after identification by Major James, I.M.S., was named after him as "Anopheles aitkeni". During his service he took to writing the Annual Reports of the Customs Department and was frequently thanked for the same. Reviewers have commented that these reports are enlivened by his witty literary touch. In the last two years of his service he was put in charge of "The Sind Gazetteer". On completion of this work he retired to Edinburgh. He died after a short illness on 25 April 1909.