Cathy Taylor, chief executive of the state’s Child Protection Department since October 2016, announced her resignation on Friday following months of intense scrutiny surrounding the deaths of two South Australian children whose families had contact with her agency.

She is set to leave the position on April 28.

Malinauskas today rejected suggestions the government had asked Taylor to resign.

“Cathy offered me her resignation on Friday and I accepted it and thanked her for a service,” he told ABC Radio Adelaide today.

“She’s got an extraordinary responsibility and one of the most complex jobs in the state to say the least.

“She’s applied her efforts as best she possibly can, and we thank her for her service.

“But her resignation of course does present a really big opportunity for my government to be able to refresh the leadership of the Department of Child Protection and apply a fresh set of eyes from that substantial role to see what else we can do to try and improve the performance of child protection in our state.”

The Premier said a process had already started to recruit Taylor’s replacement.

He said the process would be complicated by the fact the Victorian Government was also searching for a new child protection CEO.

“There is a challenge before us but we’ll do us best to find Cathy Taylor’s replacement ASAP,” he said.

“I think it will be ambitious to find a replacement and have them in the role by the end of April, but nonetheless, that’s our aspiration and we’re going be working towards that.”

He also said the state’s Child Protection Department was “going through a period of change [and] more is required”.

“Cathy’s been in the role since the Nyland Royal Commission and a lot has happened to child protection in this state since then – and not all bad, mind,” he said.

“It’s a big job and it’s complex and it’s challenging and finding someone to take on that responsibility won’t be easy, but there are people out there who are willing to do this work and we thank them for it.”

Taylor’s resignation comes after the state’s child protection system was once again in the spotlight over the past year, following the deaths of six-year-old Munno Para girl Charlie Nowland in July and seven-year-old Craigmore boy Makai Wanganeen in February.

Police are investigating whether both children, whose families had contact with the Department for Child Protection, were criminally neglected in the lead-up to their deaths.

Both deaths sparked public outcry, leading to a review by former police commissioner Mal Hyde, and a commitment by Malinauskas to conduct urgent welfare checks on about 500 South Australian children who were identified as living in “extremely vulnerable” situations.

Taylor has faced sustained questioning over her department’s involvement with the children’s families and its processes for dealing with at-risk children.

In recent years, she has also been criticised for not being aware that a 13-year-old girl in state care had fallen pregnant to a pedophile until a journalist asked the department to respond to the court sentencing remarks, which were made public.

Taylor’s department was also the subject of a review by child protection expert Kate Alexander, which was commissioned following the April release of a coronial inquest into the murder of siblings Amber Rigney, 6, and Korey Mitchell, 5.

Taylor previously worked as a deputy director-general for Queensland’s Child Family and Community Services and as a director of ANROWS – Australia’s National Research Organisation on Women’s Safety.