Bernadette Marjoram will take over the role held by Pete Leonard, who was responsible for communities, housing and infrastructure.
His duties included overseeing Hazlehead Crematorium.
Baby and adult ashes were mixed together at the crematorium and given back to relatives of the adult.
The parents of infants were told there were no ashes.
BBC Scotland revealed in 2013 that no ashes had been offered to the families of infants cremated in Aberdeen over a five-year period.
It followed similar revelations about Mortonhall crematorium in Edinburgh, which had been secretly burying baby ashes for decades.
A report into the scandal by Dame Elish Angiolini described the practices as "abhorrent".
It is understood an internal report, shown to councillors in August but then taken back by officials, was heavily critical of Mr Leonard's department in handling the scandal.
Mr Leonard did not attend the council meeting which discussed his department's conduct.
He has not been back at work since, and is on sick leave.
The council confirmed that Bernadette Marjoram had now been appointed to the role of interim director for communities, housing and infrastructure.
An interim director has been put in place at an Aberdeen City Council department criticised over the baby ashes scandal earlier this year.