Brenda Stewart was removed from her post at Polmont YOI, near Falkirk, at the end of August, according to the Daily Record.
The move came just days before Scotland’s Solicitor General, Ruth Charteris QC, apologised publicly for delays in the investigation into the suicide of Katie Allan.
The 21-year-old took her own life at Polmont YOI in 2018, while serving a 16-month sentence for a serious driving offence.
Katie’s parents, Linda and Stuart Allan, from Giffnock, claimed she had been “battered, brutalised and violated” at the young offenders institution.
They allege that Katie was forced to parade naked in front of prison officers, had lost 80 per cent of her hair through stress, and slashed at her limbs before her death.
The Scottish Prison Service (SPS) was plunged into crisis in October 2019, when the Crown Office’s decision against prosecuting the agency over Katie’s suicide was appealed by her parents through a victim’s right to review.
A Fatal Accident Inquiry into Katie’s death cannot be held until a decision is made over prosecuting the SPS.
The Allans have also previously called for Stewart’s resignation from Polmont YOI.
A source told the Daily Record: “Brenda Stewart has been under incredible pressure and there were calls for her to resign. But she hung on in there.
“She was relieved of her duties at the end of August and there is no expectation of her coming back.
“She was told Gerry Michie would be taking over the reins in the running of the jail.”
Mr Michie, from HMP Castle Huntly in Tayside, previously served as deputy governor at HMP Edinburgh.
Aamer Anwar, the solicitor representing the Allans, said: “Brenda Stewart presided over an SPS culture that thought the suicides of young people was inevitable.
"We are still fighting for the SPS to be charged with corporate homicide for the suicides of William and Katie.
“Stewart should have been held accountable for her failures a long time ago.”
A spokesperson for the SPS said: “We cannot discuss issues surrounding individual members of staff.”