When the Labour Party won power in the 1999 election, Burton became part of the new Cabinet, assuming the roles of Minister of Internal Affairs, Minister of Defence, Minister for State-Owned Enterprises, Minister of Tourism, and Minister of Veterans' Affairs. In 2002, Internal Affairs and Veterans' Affairs were transferred to George Hawkins. In February 2005 he became the Minister of Treaty of Waitangi Negotiations, and dropped the State-Owned Enterprises portfolio.