Former National Tertiary Education Union secretary Grahame McCulloch has resigned, a spokesman for administrator Mark Irving confirmed.
No reason for the surprise departure or further detail has been given.
Attorney-General Mark Dreyfus placed the CFMEU's construction and general division - including state and territory branches - into administration on August 23 following public allegations of intimidation, bribery and underworld infiltration at the union.
CFMEU boss John Setka resigned following allegations against the union. (James Ross/AAP PHOTOS)
Mr Irving was appointed as administrator and the roles of more than 200 elected CFMEU officers were terminated.
Mr McCulloch had been appointed to helm the union's Victorian branch, a role previously held by John Setka, who resigned following the allegations against the union.
Mr Setka was recently referred to police for appearing at government building sites to verbally attack the Victorian and federal governments.
Last week, Victoria Police confirmed Mr Setka wouldn't face charges over the visits, but investigations were ongoing into eight of 20 reported allegations of "potential criminal activity" against the CFMEU.
Several trade unions have announced plans to fight the decision to place the CFMEU into administration in the High Court.