Cowdery was appointed the Director of Public Prosecutions for New South Wales in 1994, and ended his sixteen-year tenure in 2011. During his term as NSW Director of Public Prosecutions he was, according to Phillip Adams "... an outspoken critic of the pace and style of drug reform, ... and of the mandatory sentencing regimes in the Northern Territory and Western Australia. With his office independent of government, Cowdery would often speak out publicly against politicians - especially if he disagreed with them. Cowdery's notable successful prosecutions include Ivan Milat, Gordon Wood, and Keli Lane.