Elected as a Liberal in the Frank McKenna landslide, Duffie continued his law practice in addition to his legislative duties.
In 1991, Duffie was re-elected as MLA and appointed to be the Minister of Education. Re-elected again in 1995 he became Minister of Municipalities, Culture & Housing. He served as acting Minister of Justice after the heart attack of Justice Minister Jim Lockyer during a game between New Brunswick and Quebec legislators.
Duffie resigned from cabinet in 1997, after considering a run for leader, to spend more time with is family. Duffie co-chaired the leadership campaign of Camille Theriault with Doug Tyler.
Duffie did not seek re-election in the 1999 general election.
In 2001, following the resignation of Theriault, Duffie was encouraged to run for leader. His biggest supporters in the small, seven member, Liberal caucus of the day were House Leader Eric Allaby and former Transportation Minister Sheldon Lee.
In early 2002, Shawn Graham emerged as the clear leader in delegate selction meetings and Duffie dropped out of the race, backing Graham.
Though he originally pledged to run in the coming election, he backed fellow Liberal and fellow former Grand Falls mayor Ron Ouellette who was elected on June 9, 2003.