It is understood senior education manager Karen Prophet was removed from her post towards the end of last year after an inquiry into how she handled claims against Derek Curran, the former head of Castlebrae Community High.
Investigators are said to have examined whether Ms Prophet acted robustly and quickly enough after receiving reports that Mr Curran, 54, had behaved in a sexually improper manner towards pupils at schools where he was employed.
Ms Prophet, previously headteacher at Firrhill High and assistant head at Inveralmond Community High, is understood to have had a close working relationship with Mr Curran.
Sue Bruce, the city council’s chief executive, is now believed to have been given a detailed report on the matter.
Ms Prophet, who is thought to take home a salary of between £70,000 and £80,000, is one of the most senior officers within the education department and has responsibility for improving schools across Edinburgh.
Her duties include ensuring teachers adhere to the new Curriculum for Excellence and making sure as many leavers as possible move on to jobs or further education.
Mr Curran last year appeared at Edinburgh Sheriff Court in connection with multiple assault charges brought by two women and was released on bail.
Dubbed a “super-head”, he was parachuted into Castlebrae in June 2013 to turn the school around after it was saved from closure amid poor exam results and falling rolls.
In a separate recent case, Castlebrae High biology teacher Gavin Atkinson, 56, was charged with sending inappropriate messages to a pupil and assaulting another student, both understood to be under the age of 16.
It is understood he has now been sacked by the city council, as the Crown Office continues to review police reports regarding charges against him.
Castlebrae High parent leaders have called on the education department to “sort itself out” as new headteacher Norma Prentice aims to improve their school.
Susan Heron, parent council vice-chair, said: “It’s the [education] department and the department should really be working to sort itself out.
“It seems to be one thing after another. We need to ensure we are getting the right people in the right places for the right reasons. I think parents at Castlebrae will probably be looking for the right people to be put into those positions to take the school forward, and build on the positives that are already in the school.”
Ms Heron added: “We need to do all we can to make sure those children become all they can be.”
A spokesman said the city council took “all complaints and allegations very seriously”.
He added: “It would be inappropriate to comment on personnel matters.”