The SNP’s chief executive, who is also Nicola Sturgeon’s husband, was challenged on the truthfulness of his evidence given to the committee on December 8.
Mr Murrell said he was merely speculating on the nature of the meeting between Ms Sturgeon and Mr Salmond on April 2, and that the committee should ask the First Minister as to whether she believed it to be party or government business.
He was also challenged on the existence of text messages between himself and other officials within the SNP on the topic of complaints against Mr Salmond, something he had said did not exist in his first evidence session.
In a tense virtual session – hampered by technology with committee members speaking over Mr Murrell and vice versa – Mr Murrell said many questions were “drifting into conspiracy theories”.
Jackie Baillie, Scottish Labour’s spokesperson at the inquiry, pressed Mr Murrell on his evidence there were no additional text messages concerning complaints against Mr Salmond that he was involved in.
Ms Baille has previously called for a perjury investigation into Mr Murrell on the basis of his evidence in December, with questioning along those lines put to Mr Murrell throughout the session.
She asked the SNP boss whether he stood by his position there were no other text messages, to which he replied “You asked whether there was any relevant information and there wasn’t and there still isn’t.”
Ms Baille responded, stating she had asked about any other text messages relating to allegations against Mr Salmond.
She asked: "Are you saying your testimony then was correct?”
Mr Murrell responded: “You’re saying it is clear, I would say it is confused. You say other party official, you don’t say the same party official.
"The basis on which I asked staff whether there were any relevant messages was the committee’s remit and each of them came back and said they didn’t have any messages that were relevant to the inquiry.”
Ms Baille added: “I think people watching will see that Mr Murrell is dancing on the head of the pin. He made no such caveats to his evidence previously and I think this is becoming quite obstructive to the work of the committee.”
Mr Murrell was also asked whether he recognised a message he had sent to a senior officer on January 29, 2019, which expressed dissatisfaction the officer was “not being forceful enough to achieve the objective of having her make a police statement”.
In response, Mr Murrell said: "There is a danger in pulling information from social media, selectively quoting information, leaking and false allegations.
"That is not the context of that message and again we’re drifting into an area where we are invading the privacy of someone we know already we have caused a great amount of stress to.”
Asked when he became aware of a complaint from the Crown Prosecution Service about a incident in London, Mr Murrell said he could not answer how he came to be aware of the complaint due to it invading a complainant’s privacy.
Earlier, he had been asked whether he stood by his statement the nature of the meeting on April 2, 2018 was a Scottish Government matter.
The SNP chief executive said his response had been “speculation”.
Scottish Conservative member on the inquiry, Murdo Fraser, put it to Mr Murrell that he had been “definitive” when asked the same question in December.
In response, Mr Murrell said: “Well, I think as I have already said, speculation on my part having read her evidence.”
Audibly frustrated, Mr Fraser replied: “I am afraid Mr Murrell, having called you back to try to clarify your evidence that you are not helping one little bit. You haven’t clarified anything, frankly.”
Asked whether he had been untruthful in December when he said he had not been at home during the meeting, Mr Murrell replied he “absolutely refuted” the suggestion he had lied to the committee.
"I have no idea how long the meeting lasted,” he said.
"I wasn’t here for any part of the meeting. I happened to arrive home just as the meeting was finishing.
"That’s all I can say, it is not complicated, I absolutely refute what is being suggested. I just happened to arrive home as the meeting was ending.”
Liberal Democrat Alex Cole-Hamilton also asked about the meeting and questioned Mr Murrell on whether any discussion had taken place between him and Ms Sturgeon about its nature.
Mr Murrell said he understood Mr Salmond was “just popping in” and said, in response to questions on why he had not been informed of the fears from the First Minister that Mr Salmond could be resigning from the SNP, that “you deal with [issues] as they come down the track at you”.
In response, Mr Cole-Hamilton said he “just doesn’t find it credible” the married couple hadn’t discussed the issue prior to the meeting.
Ms Sturgeon will give evidence to the committee next week, with Mr Salmond confirming this morning he will not attend the session on Tuesday morning.
The committee is examining the botched handling of harassment complaints against the former first minister by the Scottish Government, which led to a £500,000 legal bill after the government conceded a judicial review challenge on the grounds of the process being “tainted by apparent bias”.
Mr Salmond was also acquitted of sexual offence charges in a trial last year.