In March 1853 Clarke was asked to replace Robert Hoddle as Surveyor General of Victoria and arrived at Melbourne in May. His hard work and energy resulted in more land being sold in the next 18 months than in the years since 1836. He also established the Roads Boards that preceded the introduction of local government and was responsible for much of the planning of Victoria's first railways. His proposals for a government-controlled railway system were examined by a select committee and were made law in 1857. Additionally, he set up the first electric telegraph from Melbourne to Williamstown, Victoria and was able to report in November 1857 that the service had reached the borders of New South Wales and South Australia. In 1855 he was elected the inaugural president of the Philosophical Institute of Victoria.