Dave Anderson, who was sent home by Edinburgh City Council earlier this year from his role as head of city development, is the second senior figure to leave the council during the investigation. Earlier, Brian Sibbald reportedly stepped down as head of property conservation for health reasons.
There was no suggestion of fraudulent behaviour by Mr Anderson, but The Herald revealed at the time of his suspension in June that a source who saw a confidential account of his handling of the corruption claims said his response was "woefully inadequate".
The council would not say how many people involved in the investigation into the property conservation department, overseen by city development, have now departed.
It would also not comment on whether the probe identified concerns over Mr Anderson's management of the claims.
Fifteen people have been charged in connection with a wider police inquiry into the council's property services department.