John Swinney’s comments come after the publication on Tuesday of the Holyrood inquiry into the Scottish Government’s handling of harassment complaints against Mr Salmond.
The report found several major failings in how the Scottish Government handled the judicial review action brought by the former first minister.
It also concluded Nicola Sturgeon had misled the committee, and by extension the Parliament, over the nature of the meeting between her and Mr Salmond on April 2, 2018, with the committee believing she did offer to intervene – a position denied by the First Minister.
The inquiry report is the final of three reports on the Scottish Government and First Minister’s conduct during the affair following the publication of the Laura Dunlop QC review of the procedure itself and the James Hamilton report into a potential breach of the ministerial code by Ms Sturgeon.
Reacting, Mr Swinney welcomed the report and repeated the Scottish Government was sorry that it “made mistakes” and for the “real and damaging impact” on the women involved.
He said: “I welcome the report of the committee, which, alongside the independent report produced by James Hamilton and externally led review by Laura Dunlop QC, will assist the Scottish Government’s in learning lessons for the future.
“I also welcome the committee’s acknowledgement that the Scottish Government was motivated by doing the right thing, creating a culture and procedure for investigating any claims of harassment.
"I agree with the committee’s finding that James Hamilton’s report is the most appropriate place to address the question of whether or not the First Minister breached the ministerial code. He found there was no breach.
“The Scottish Government has acknowledged that it made mistakes and that these led to the judicial review being conceded, and I know that this had a real and damaging impact for the women who raised the complaints. We have apologised for this and we do so unreservedly again today.”
However, the deputy first minister did not indicate whether the Scottish Government would follow all of the recommendations in each of the reports and said it was “not possible” due to the timing of the reports to issue a full and detailed response.
Mr Swinney said: “I remain absolutely determined that the Scottish Government should ensure this does not happen again and that together we create a culture where these behaviours do not arise.
“Given the timing of the report, it is not possible to respond fully and in detail, not least because the three reports have overlapping areas of interest, and some recommendations are in conflict with those in other reports.
“Together, all three reports highlight a range of important issues and provide the basis for improvement work which now be taken forward in consultation with others including the Parliament, trade unions and those with lived experience.
“The Scottish Government will carefully consider the recommendations from the committee, alongside the other two review reports, in order to put improvements and an implementation plan in place.”