The company has also dismissed former Observer editor Andrew Jaspan as editor of The Age in Melbourne.
The job cuts equate to about 5% of the company's total workforce and will mean the loss of 60 journalists from The Sydney Morning Herald and 50 at The Age, according to a report in The Australian.
Fairfax, which is being accused of abandoning quality journalism by staff, also announced it would outsource production of some of the sections and special reports that are inserted into its papers.
The restructuring comes following a downturn in print ad revenues at the company.
Jaspan, who has also edited the Sunday Times Scotland, Scotland on Sunday, The Scotsman, and the Sunday Herald, leaves The Age after a four-year stint as editor-in-chief.
He has been replaced by senior deputy editor Paul Ramadge, who takes over as acting editor-in-chief while a permanent successor is found.
Don Churchill, chief executive and publisher of Victorian metropolitan and community publishing at Fairfax, said: "Andrew has been a highly successful editor. He has delivered great papers and has done a magnificent job in reinvigorating The Age.
"He has our thanks and appreciation for all he has achieved in the past four years. Under Andrew's editorship, The Age benefited from an innovative redesign and consistent, strong growth in circulation and readership, and agenda-setting journalism.
"The Age was named Newspaper of the Year by PANPA in 2007, one of the industry's highest honours. The company is discussing with Andrew the ways his skills and expertise can be made available within the company.
"The company has decided that for this next critical stage of The Age we would have fresh editorial and executive leadership."
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