The First Minister said she took responsibility for the actions of the Scottish Government and the failures, saying that it was important to recognise the organisation was “trying to do the right thing”.
Pressure on Leslie Evans, the permanent secretary, to resign has been mounting in recent months and grew further following the publication of the Holyrood inquiry into the Scottish Government’s botched handling of harassment complaints against Mr Salmond.
The report detailed a litany of failures within the Scottish Government, including a failure to meet its duty of candour to the Court of Session and failing to see the risk in appointing a civil servant with extensive prior contact with complainers to a position that required none.
Jackie Baillie, the Scottish Labour member of the Holyrood committee, said at First Minister’s Questions on Wednesday that she did not believe Ms Sturgeon was “happy” with the way her government had acted.
She said: "The First Minister has acknowledged the catastrophic failure of the Scottish Government in the handling of harassment complaints and I welcome the First Minister’s comments.
"The development of the policy was flawed, the appointment of the investigating officer was wrong and even documents were withheld from the Court of Session.
"I do not believe the First Minister is happy with any of that, so why three years on has no-one assumed responsibility?
"Why does the First Minister still have confidence in the permanent secretary, who presided over all of this terrible mess.”
Responding, Ms Sturgeon said she had taken responsibility for the failures of the Scottish Government despite not resigning.
Her comments came after a spokesperson said the First Minister still had confidence in Ms Evans as her top official.
Ms Sturgeon said: “I take responsibility for what happens within the Scottish Government and I take responsibility for acknowledging when things go wrong and also for putting right things that go wrong.
"Few things matter more to me than making sure we have a culture within the Scottish Government where anybody who believes that they have been subject to harassment can come forward and have confidence and trust that their complaints will be listened to and addressed properly.
"The government did make a mistake in this and I have certainly never shied away from that, but I will also never shy away from saying this – it made a mistake in the course of trying to do the right thing because unlike what would have undoubtedly happened in years gone by, complaints by this would not simply be swept under the carpet.
"That’s the right starting point. What we have to do now is put right the things that went wrong, so mistakes are not made in the future.
"I deeply regret and have apologised and will continue to apologise to the women who were let down.
"My final point is this, and I don’t say it in an adversarial sense, but I hope Jackie Baillie will also reflect on the fact that the committee, in doing its important work, also let down women in leaking misrepresentations of their evidence.”