Hamm's Tories defeated the Liberal minority government on a budget vote on June 17, 1999, and in the subsequent election on July 27, 1999, Hamm was elected Premier, winning 30 of the 52 seats in the provincial legislature. After taking office, Hamm sold or closed government-owned industries such as Sydney Steel. He invested more in education and health care, and implemented some tax cuts. His government was the first to truly balance provincial finances in 25 years, following changes in public sector accounting practises. In 2001, Hamm was at odds with the Nova Scotia Government Employees Union, trying to legislate nurses back to work after a legal strike. In the 2003 election, Hamm's Progressive Conservatives were reduced to a minority government. The main issue in that election was the increasing cost of car insurance and whether Nova Scotia should begin to allow general Sunday shopping. Despite the minority government, Hamm's government was able to drop an NDP plan for government automobile insurance issue, and put the Sunday shopping issue to a province-wide plebiscite. Hamm is opposed to Sunday shopping and a public auto insurance system.
On December 21, 2006, Hamm was appointed Chairperson of Assisted Human Reproduction Canada, a federal agency created to protect and promote the health and safety, human dignity and human rights of Canadians who use or are born of assisted human reproduction technologies, and to foster ethical principles in relation to assisted human reproduction and other related matters. In 2009, he was made an Officer of the Order of Canada "for his contributions to the province of Nova Scotia as a former premier, family physician and community leader." In 2010 he became the Chairman of the Board of the holding company for Northern Pulp mill of Abercrombie, whose board he had joined shortly after his resignation from politics prior to the 2006 provincial election. In May 2014 he was awarded a Doctor of Civil Law from University of King's College, Halifax, Nova Scotia for his service to King’s, his community and the province. October 2014, he was awarded an "Honorary Fellow of the Royal College of Physicians and Surgeons of Canada." Also in October 2014, John Hamm was appointed the Honorary Colonel for the 1st Battalion Nova Scotia Highlanders for the next three years.
Atlantic Accord
One of his most notable achievements was negotiating with the federal government to implement the Atlantic Accord, a multi-decade regional development program that had been approved in principle during the late 1980s to prevent provincial government offshore oil and gas royalties from being included in calculations for the federal equalization program. This resulted in an $830 million payment in 2005 from the federal government, which Hamm applied against the principal on the province's long term debt, thereby reducing debt servicing payments by over $50 million annually.