The duties of the ship surgeon ranged from inspecting the emigrants before boarding (he had to sign a certificate attesting to their good health), to ensuring that there was efficient air circulation throughout the ship. The Instructions to Surgeons Superintendents of Government Emigration Ships (1866) lay out the extensive rules for how a surgeon should appropriately act and what came with the job. Another popular book of guidelines was Handbook for Surgeons Superintendent in the Coolie Emigration Service (1889), by James M. Laing, a skilled and retired surgeon superintendent. Whether certain individuals actually followed these guidelines remains very unclear.
According to these instructions, not only was the surgeon responsible for maintaining the health of those on board, but also for disciplining them when he saw fit.; this may be where the issues of too much power originated from. The surgeon would also inspect the “Cooking Apparatus” and also carry around a “Water Con-Distilling Apparatus” so that he was able to convert saltwater into something more “fresh.” Surgeons were required to keep a detailed journal and record of the voyage and patients as well as visit the decks at least two to three times a day to ensure cleanliness and preserve dryness (no laundry, washing, or anything that required water was allowed on the decks).
In 1857 their pay was increased to 10s per every person who arrived alive (an increase from their previous 8s). On every subsequent voyage, this amount per “head” would increase 1s up to 12s. Increasing the surgeon’s pay was a good way to attract more competent individuals for the job.

 
Note: While these images are from Australian surgeons, it is expected that the surgeons aboard The Clarence and other ships would use similar materials.