Peter Fray, the editor-in-chief of the Sydney Morning Herald, is also stepping down, along with the Herald's editor Amanda Wilson, senior Sydney Morning Herald reporter Sean Nicholls said on Twitter.
The upheaval comes only days after Fairfax Media announced 1900 job cuts across the flagship newspapers.
The Sydney Morning Herald online later reported the Mr Fray and Ms Wilson had announced they were leaving the company.
In a statement to the SMH online, Fairfax Metro Media Editorial Director Garry Linnell said two distinguished Fairfax careers were ending with their decision to leave.
"We are saying farewell to two champions of our profession," he said.
Two new appointments were expected to be announced later on Monday, Mr Linnell said.
The Age was also expected to announce new appointments.
The website said Ms Wilson announced her departure in an emotional address to the newsroom, saying a major newsroom review was about to take place and it was time for her to pursue new challenges.
Mr Fray told colleagues he did not have a new job to go to but saw his resignation as an exciting opportunity.
- AAP