He was employed as Surgeon-Superintendent on only one convict ship to Australia - the Canada in 1817.
The Canada departed Cork on 21st March 1817 and arrived in Port Jackson 5th August 1817. Eighty-nine female convicts and eleven children; two free passengers and three children arrived on the Canada under his care. There were no deaths on the voyage out.
He informed Governor Macquarie in correspondence dated 12 September 1817 that he had taken every precaution to prevent prostitution of any female convict from the time they embarked on the Canada and during the voyage. To the best of his knowledge no female had lived with any Officer on the vessel during that time. 
Departure from the Colony
James Allan departed the colony on the Canada in October 1817 bound for Batavia.
In 1832 James Allan donated a box containing specimens of petrifactions found in the neighbourhood of English Harbour, Antigua, and some specimens of copper ore from Jamaica to the Naval and Military Museum
He was appointed surgeon to the San Josef, Plymouth 1st January 1833 
James Allan (a) M.D. was appointed to the Haslar Hospital 7 December 1839 as Surgeon and Medical Storekeeper. - The New Navy List. His name is included in the 1841 Census, place of residence, Haslar Hospital. Age 45.
James Allan (a) M.D. was appointed Deputy Medical Inspector at the Royal Hospital Haslar 4th February 1845.
He died at Portsmouth in 1851.
Notes and Links
1) Popliteal Aneurism Cured by Pressure. By James Allan of The Royal Hopsital, Haslar. Published in the Lancet 18 January 1845