The Crown Office faced criticism last week after it intervened at the 11th hour around the publication of the former first minister's evidence submission on the potential ministerial code breach by Nicola Sturgeon.
The decision to intervene, which led to the Scottish Parliament removing, redacting and republishing the submission, has led to calls for the dual role held by the Lord Advocate to be split up due to the potential for conflict.
In his evidence session on Friday, Mr Salmond had also called for the Lord Advocate, James Wolffe QC, to “consider his position” and urged a refresh of leadership at the Crown.
During his evidence session alongside Crown Agent David Harvie at the Salmond inquiry on Tuesday morning, Mr Wolffe defended the independence of the Crown and labelled accusations of political influence as “wholly without foundation”.
In his opening statement, he said: “Comments have been made about the Crown which are without foundation and the public is entitled to hear the truth about these matters from me.
“Any suggestion from any quarter that the Crown’s decision making has at any time been influenced by irrelevant considerations or improper motivations would be wholly without foundation.
"Insinuations or assertions to the contrary are baseless.”
Answering questions on the different levels of redaction requested by the Crown to Parliament compared with The Spectator case, Mr Wolffe said the content was “revisited” when Holyrood published the submission and additional areas of concern were raised.
He said that in cases of contempt, the Crown would raise concerns, but that it was up to publishers to determine what was at risk of being contempt.
Mr Wolffe said the Crown “cannot give a clearance or assurance because it is not in the Crown’s gift to determine whether or not a particular article is or is not a contempt”.
The Lord Advocate was also asked about the potential for “tension” in his dual role as head of the prosecution service and as a Cabinet minister as chief legal adviser to the Scottish Government.
Responding, Mr Wolffe said the Lord Advocate role had held the dual role since prior to devolution.
He said: “I think any suggestion that it cannot be held with integrity is wrong.
"I am satisfied that the different responsibilities and functions can be combined with integrity.
"My fundamental, my only responsibility is to the rule of law and the administration of justice.”
Mr Wolffe was also pressed on the Crown’s threatened use of section 162 of the Criminal Justice and Licensing (Scotland) Act 2010, which Mr Salmond claims has been used improperly to keep relevant evidence from the committee.
In his opening statement, he said: “It is the law, not the Crown, that stays his hands.
"Enforcing the law, including the law laid by this Parliament, is a vindication of democracy, not its denial.
"Any suggestion that the professional prosecutors who are charged with these matters have been acting for any reason other than to ensure that the law is observed and to protect the administration of justice would be wholly without foundation.”
In a lengthy session, the Lord Advocate was also pressed on the claims from Mr Salmond the Scottish Government failed to respond appropriately to a search warrant.
Mr Salmond had claimed around 40 documents were not disclosed, but Mr Wolffe would not be drawn on whether such a failure would constitute a criminal offence.
He said the Crown had not been notified of any such concerns.
The committee 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 in a trial last year.
The First Minister will give her evidence to the committee on Wednesday morning from 9am.