In September 1999 Bracks polled surprisingly well in the election, and three rural independent members gave Labor the opportunity to govern as a minority government. As Deputy Leader, Thwaites became Deputy Premier and was given the senior Health portfolio, with a mandate to increase funding to the public health system which had been the subject of cutbacks under the Liberal government. He was also Minister for Planning from 1999 to February 2002. Shortly after taking office, Thwaites cancelled the proposed privatisation of the Austin Hospital and announced plans for the government to rebuild the hospital with public funds. (“Labor to cancel Austin hospital privatisation” The Age 28 October 1999)   (“Can the new government fix health? The Age 20 November 1999). Like all state health ministers, he had only limited success in reducing waiting lists at public hospitals, but did succeed in restoring the numbers of nurses.