Following the resignation of Deputy Prime Minister and Nationals leader Tim Fischer, Anderson was elected unopposed as the new leader and become Deputy Prime Minister himself on 20 July 1999. Anderson kept his ministerial responsibilities in Transport and Regional Development and were extended to the delivery of government services, such as health, to regional and remote centres, and a role in the National Security Committee. Anderson also assumed the role of Acting Prime Minister when John Howard was overseas, such as during the September 11 attacks and in the aftermath of the 2002 Bali bombings.