A shakeup is occurring at South Australia's new Child Protection Department.

The department was set up in the wake of last year's damning Nyland royal commission into the child protection system, with Cathy Taylor appointed CEO.

But it is now being restructured, making Families SA deputy chief executive Etienne Scheepers redundant while executive director Rosemary Whitten has retired after 40 years’ public service.

Mr Scheepers was appointed deputy chief executive (Child Safety) in 2014 after previous executive David Waterford resigned in the wake of paedophile carer Shannon McCoole's arrest.

At the time of his appointment, Mr Scheepers was described as bringing a wealth of experience to Families SA.

“Etienne Scheepers is an outstanding public administrator who has a proven track record in implementing complex reforms that improve the level of services provided to the public,” then department chief executive Tony Harrison said.

The Nyland royal commission called on Families SA to be reformed in order to make a “fresh start”.

“I hope that this new child protection department with a refreshed leadership will establish a much improved system to keep children safe from harm, and restore public confidence,” Ms Nyland stated in her report.