 Apart from a short period doing contract surveying for the New Zealand Company in March 1849, Brunner remained unemployed and wrote numerous letters to his contacts. His former travelling companion, William Fox, and Dillon Bell, chief agent of the New Zealand Company, also sought to find him a job and through them, he was able to find work as a clerk with the Canterbury Association between September 1849 and February 1850. He returned to Nelson in May 1850 and secured full-time employment as a surveyor with the New Zealand Company, but with the proviso that he would be able to take on private work which did not interfere with his duties. To supplement his income Brunner began to take on architectural commissions.
