Responding to an urgent question in Holyrood’s chamber on Wednesday from Scottish Labour’s Jackie Baillie, James Wolffe QC said the Crown had “no interest in interfering" with the Parliament’s business.
His declaration comes as the Holyrood inquiry investigating the botched handling of sexual harassment complaints against the former first minister decided to write to the Crown Office demanding messages referred to by Mr Salmond in his final submission.
The second use of a section 23 order, which will compel the Crown Office to provide the evidence, is understood to be a direct response to Mr Salmond’s allegations of conspiracy.
The move comes after Mr Salmond agreed to appear in front of the committee on Friday, setting up a dramatic end to the inquiry over the next seven days.
The Lord Advocate has been invited to give evidence on Monday, with the First Minister to be the final witness on Wednesday.
Ms Baillie asked the Lord Advocate whether he was consulted before the decision to intervene was made and whether he was made aware of the decision.
In response, Mr Wolffe said: “No I was not. The decisions in relation to this matter were made by senior professional prosecutors acting independently as they always do and without reference to the law officers.
"Scotland's public prosecutors take difficult decisions that some may find unpopular. They take those decisions objectively, professionally and in the public interest and they act independently of any other person."
Mr Wolffe said he received a copy of the letter sent to the Parliament “for my information” after it had been sent.
However, he failed to answer a question on whether the Crown Office had received any third party submissions around the issue.
He also did not answer why the Crown Office’s opinion on the extent of the necessary redactions had changed since the hearing brought by The Spectator in front of Lady Dorrian earlier this month.
Reacting, Ms Baillie labelled the Lord Advocate’s reticence to answer questions in detail “simply unacceptable”.
She said: “The news that he was not consulted about the letter from the Crown Office to the Scottish Parliament Corporate Body (SPCB) brings us no closer to understanding the Crown Office’s actions.
“The fact of the matter is that the Parliament is not getting straight answers from a Lord Advocate who appears to have viewed this afternoon’s session in the chamber as a necessary chore and not a chance to engage with the Scottish Parliament in a spirit of democratic accountability.”
Donald Cameron of the Scottish Conservatives pressed the Lord Advocate as to whether the actions of the Crown “threatened the freedom” of the Parliament to conduct its business without external pressure from government agencies.
Mr Wolffe said: “The Crown has no interest in interfering with or limiting the conduct of proceedings in this Parliament.
"It’s only interest is securing observation and compliance with an order of the High Court, with which we are all obliged to comply whether in this Parliament as otherwise.
"As with any anticipated publication which may amount to contempt of court, the Crown considered whether it should raise concerns with parliamentary authorities. It took the view that it should.
"It was ultimately a matter for the parliamentary authorities taking their own legal advice to determine what they should or should not publish.
"The Crown, having raised the concerns which it has raised, has exhausted its interest in this matter and has absolutely no interest in otherwise limiting the activities or conduct of business in this Parliament.”
In response to a written question, David Stewart MSP said the SPCB was unable to publish the letter from the Crown and had decided some of Mr Salmond’s submission should be redacted.
He said: “The SPCB takes it duty to support parliamentary scrutiny and to promote public transparency very seriously indeed, but is acutely conscious of the need to act lawfully in all circumstances.
"These obligations do not always necessarily sit comfortably together.”
The Lord Advocate’s appearance came as the Salmond inquiry released details of its next steps, which include demanding further evidence from the Crown Office and asking the Scottish Parliament to test the legality of publishing the former first minister’s submission in court.
Mr Salmond claims the evidence still held by the Crown Office would prove the existence of a conspiracy to get him jailed by senior members of the SNP and members of the Scottish Government.
The inquiry has also requested the SPCB request official guidance from the High Court on whether Mr Salmond’s evidence submission on the ministerial code breaches Lady Dorrian’s contempt of court order.
It is understood there is disquiet around the reaction from the Crown Office on Monday given the fact The Spectator’s version of the evidence remains online.
Such a move would see the legality of the revised submission tested in court and could put its admissibility beyond doubt.
Alex Cole-Hamilton, who moved the motions calling for both actions, said the inquiry had a “duty” to request and examine the messages.
He said: "At the end of the day it is not for the Crown Office to determine what our remit is where other text messages or other communications are relevant to our work.
"We have been given a clear steer from a key witness that the evidence for the astonishing allegations he is making lies in these messages.
"We have a duty to follow that lead and would expect full co-operation from the Crown Office."
The inquiry is examining the botched handling of harassment complaints against Mr Salmond by the Scottish Government, which led to a £500,000 legal bill after the Government conceded a judicial review challenge on grounds the process was “tainted by apparent bias”.
Mr Salmond was also acquitted of sexual offence charges last year.