Derek Curran, 53, was removed from his post at Edinburgh's Castlebrae Community High School, Craigmillar, after claims of sexual misconduct in June.
The probe was expected to focus on his time in charge at the capital's Forrester High, where he previously worked for six years.
Mr Curran now faces allegations of domestic abuse that are understood to have been made by two women, while police confirmed there was an "ongoing investigation". He has not been charged with any offence.
Susan Heron, vice-chairwoman of Castlebrae Community High parent council, said: "It's really nothing to do with Castlebrae, as he is no longer there. I hope we can put this fiasco behind us and move on."
Mr Curran joined Castlebrae Community High last summer to oversee the secondary and its feeder primary schools.
He was charged with turning around the school after council chiefs pulled back from controversial plans to close it amid poor exam results and failing rolls.
Officials had recommended the school - which had some of the worst exam results, truancy and exclusion rates in Scotland - should close, with pupils moved to other secondaries.
Mr Curran has been credited with leading a revival in the school's fortunes, after introducing a range of measures to boost the once-failing institution.
But he was suspended at the beginning of last month as a "precautionary measure" while education bosses investigated claims of sexual impropriety with a student.