John White returned to England on leave, Balmain was recalled to Sydney as acting Principal Surgeon. He and his family left Norfolk Island in August 1795. Much of the stock they left behind was destroyed in a gale the next month. Later years in Sydney In May 1797, following White's resignation, Balmain was appointed Principal Surgeon of the Colony. By this time there were 1600 settlers and several thousand convicts, but Balmain had only one assistant surgeon and found the task of caring for the health of the entire population arduous and frustrating. He petitioned the new Governor, John Hunter for assistance and an increase in salary but was rewarded only by appointment as Civil Magistrate in New South Wales. One of his first tasks was to sit on the court of enquiry in May 1797 into the treatment of convicts on the Britannia. He made recommendations for better medical treatment on board the transports, but these were not adopted. Governor Hunter described him as "an active and spirited magistrate". In his role as magistrate he had the challenging task of maintaining an uneasy peace between the often arrogant soldiers of the New South Wales Corps and the settlers, both free and emancipist (ex-convicts). This resulted in the affair of John Baughan, a settler who had tried to set up a flour mill. In February 1796, soldiers and officers destroyed Baughan's house and threatened his life and, when Balmain promised protection to Baughan and urged him to give evidence against the soldiers, the Corps expressed indignation at what they regarded as his "shamefully malevolent interference in the affairs of the Corps. The affair became a test of strength between the colony's civil authority, represented by Balmain, and the military, represented by Captain John Macarthur. In the end, the matter was dropped (following Balmain's withdrawal of his challenge to a duel), and Balmain received a small salary increase. The New South Wales Corps remained a thorn in the side of Governors and the civil authorities for the next 15 years. Although two other magistrates were appointed, their ill-health meant that Balmain shouldered most of the responsibility, as well as his medical duties. This began to affect his own health, and in July 1800 he requested to return to England. As Hunter was finding his services indispensable, the request was refused. Among other civic duties, Balmain was a member of the Orphan