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.

The second-tier club, located just east of capital city Brussels, narrowly avoided relegation this season.
The club's board set a time limit in its search for investment and said King Power "was the only bidder who made a clear and coherent proposal".
Its directors said the deal "guarantees the future of the club, both financially and in sporting terms".
OH Leuven were relegated from Belgium's top tier in 2015-16 but said new ownership would provide "sufficient financial resources to aspire to the earliest possible return".
It added King Power - founded by Leicester chairman Vichai Srivaddhanaprabha in 1989 - will fund an expansion of the club's youth system.
The acquisition will be formally completed when the company has concluded due diligence.
Srivaddhanaprabha is worth an estimated £3.6bn according to Forbes.
The 58-year-old bought Leicester in 2010, with the club winning promotion to the top flight four years later and claiming the Premier League title in 2015-16.
An interim director has been put in place at an Aberdeen City Council department criticised over the baby ashes scandal earlier this year.
[NEXT_CONCEPT]
Leicester City owners King Power International have agreed to purchase OH Leuven, the Belgian club says.