Nova Scotia Premier Stephen McNeil says David Darrow, his deputy minister and clerk of the executive council, will leave his post on Dec. 31.
McNeil put Darrow in charge of the schooner's rebuild earlier this year amid the project's growing costs and missed deadlines.
The project reached a crucial milestone Tuesday when the vessel's newly completed hydraulic steering system was unveiled for the media.
Darrow's career also included overseeing the development of a remediation plan for the Sydney tar ponds and coke ovens site as CEO of the Sydney Tar Ponds Agency.
As well, Darrow served as deputy minister of transportation and infrastructure renewal between 2005 and 2011.
Catherine Blewett, deputy minister of intergovernmental affairs and CEO of the Office of Immigration, will take over as McNeil's deputy minister.