A restructured management approach that has put more onus on staff is paying dividends for farm managers Isaac and Michelle Johnstone.
Ms Smith will not be replaced, her responsibilities instead being absorbed by existing employees.
"With the recent changes to the Board and senior management team it is an opportune time for a new team to carve out the next chapter for Murray Goulburn,” Chairman Philip Tracey wrote in a letter to suppliers.
"After making an outstanding contribution to the company since joining in 2012, Fiona leaves Murray Goulburn with the Board’s and senior management team’s sincere gratitude and best wishes.”
The company also announced the appointment of former Coca Cola Amatil executive Mark Clark to the board as non-executive director.
Mr Clarke replaces Peter Hawkins whose departure was announced at the company AGM last month.