Salmond called on Scotland’s top civil servant, Permanent Secretary Leslie Evans, to quit following the collapse of the government’s case at the Court of Session in Edinburgh yesterday amid flaws over the way allegations concerning the former SNP leader were investigated.

There are now concerns that women may be discouraged from coming forward to report future harassment as a result of the “procedural flaws” that brought down the government investigation yesterday.

The case is likely to cost taxpayers somewhere in the region of £500,000 in legal bills after Salmond was awarded full costs. He has also declared he is also considering suing the government he once led.

First Minister Nicola Sturgeon made a statement at the Scottish Parliament yesterday. Picture: PA

But the allegations themselves, dating from Salmond’s time as First Minister, have not gone away.

Salmond’s case focused entirely on the fairness of the government’s procedures and will have no bearing on a separate police inquiry into the allegations, which is still ongoing.

The police inquiry has already seen a number of Scottish Government officials and SNP staff interviewed.

Ms Sturgeon is facing awkward questions after it emerged she had a series of meetings and phone calls with Salmond during the inquiry where he set out his “concerns”.

The SNP leader said she did not feel “under pressure” to intervene despite confirming she had met with Salmond three times after complaints were made against him.

Two of those meetings – one on 2 April and the other on 7 July – were at her home in Glasgow. The other took place on 7 June ahead of the SNP conference in Aberdeen.

Ms Sturgeon told MSPs yesterday: “I want to express my regret in particular for the difficult position that the complainants have been placed in.

“I can only imagine how difficult the decision to raise concerns, as well as the publicity around this investigation and the judicial review, must have been for them in recent months.

“They had every right to expect the process to be robust and beyond reproach in every aspect of it, to reach a lasting conclusion.

“I am sorry that on this occasion, this has not been the case.”

Ms Sturgeon revealed she had not spoken with Salmond in almost six months. She spoke to him by phone on both 23 April and 18 July.

The case against Salmond came to light in August after two complaints were made in January of last year.

This followed a new procedure introduced by the government to investigate harassment claims following the fallout of the global #MeToo movement.

Salmond immediately challenged the process used and won his case yesterday after it emerged the government’s investigating officer Judith Mackinnon had previous contact with the women involved about their complaints.

Lord Pentland found yesterday this was “unlawful” and may have the appearance of bias.

Salmond was accompanied in court yesterday by former SNP justice secretary Kenny MacAskill and former Holyrood presiding officer Tricia Marwick.

He said afterwards: “The last time I was in that court it was to be sworn in as First Minister of Scotland.

“I never thought it possible that at any point I would be taking the Scottish Government to court – and therefore while I’m glad about the victory which has been achieved today, I’m sad that it was necessary to take this action.

“The consequences are very clear. Because the process has been agreed as unlawful, as unfair and tainted by apparent bias, then the Scottish Government have had to concede on the case and the expenses to the maximum extent.

“That is going to raise a cost to the public purse of many, many hundreds of thousands of pounds.

“And all of this was unnecessary because throughout the process we offered mediation, legal arbitration, so that this matter could be properly settled without having to come to the highest court in the land.

“At every stage that was rebuffed by the Permanent Secretary.”

Salmond added: “I suggest the Permanent Secretary now accepts that responsibility and considers her position.”

He described the Scottish Government’s climbdown as an “abject surrender”.

Ms Evans, who established the procedures which were used to investigate Salmond, refused to quit.

But she apologised and ordered a review into what went wrong.

The climbdown came after the government had issued a series of robust statements insisting it was ready to defend its position in court.

“The full picture only became evident in December 2018 as a result of the work being undertaken to produce relevant documents in advance of the hearing,” Ms Evans said yesterday. “I want to apologise to all involved for the failure in the proper application of this one particular part of the procedure.

“There is nothing to suggest that the investigating officer did not conduct their duties in an impartial way.

“Unfortunately, the interactions with the complainants in advance of the complaints being made meant that the process was flawed, however impartially and fairly the investigating officer conducted the investigation.”

Ms Evans said the court case was “never about the substance of the complaints”, but about the process that took place to investigate those complaints.

“It is accordingly open to the Scottish Government to re-investigate the complaints and, subject to the views of the complainants, it would be our intention to consider this,” she said. “However, this will only be once ongoing police inquiries have concluded.”

Civil service union the FDA called for the case to be reopened. General secretary Dave Penman insisted the fall of the case was down to a “flaw” in the way it was conducted.

“It does not challenge the process itself or make judgement on the substance of the case,” he said.

“In these circumstances, subject to the wishes of the complainants, we would call on the Scottish Government to re-investigate the complaints at the most appropriate time.”

But there are growing concerns the collapse of the case could stop future victims coming forward.

Tory MSP Annie Wells said: “At the centre of this entire affair are two women whose complaints against the former First Minister have now fallen apart thanks to the incompetence of the Scottish Government. It’s a complete shambles. The Permanent Secretary has apologised for her role in this fiasco, but it is Nicola Sturgeon who must take responsibility.”

She added: “Her government has presided over a mess which only risks discouraging women from coming forward in future. It is a disgrace.”

Labour’s Pauline McNeill said: “We must not forget that this case is fundamentally about women and the bravery it takes to come forward to challenge powerful men and powerful institutions. The Scottish Government must take steps to ensure this could never happen again.”

Nicola Sturgeon apologises after flaw found in Alex Salmond investigation