Sir Lindsay Hoyle's position as Speaker looks untenable, Humza Yousaf has said.
The First Minister said there were "serious questions to answer" about the "frankly disgraceful, chaotic scenes" in the Commons on Wednesday night.
The SNP leader's comments came as Stephen Flynn called for a vote of no confidence.
He said yesterday's debate on a motion calling for an immediate ceasefire in Gaza had "descended into farce" because of Sir Lindsay's decision to overrule his clerk and push Labour's amendment to a vote.
READ MORE: Flynn calls for probe into Speaker's meeting with Starmer
Speaking in the Commons following a private meeting with the Speaker, Mr Flynn said that meant that he and his colleagues were "denied the ability to vote on the matter, which is of grave concern to us, and which over recent months, we have sought to raise in this chamber, every available opportunity."
He said it had ultimately turned an SNP opposition day into a Labour opposition day.
"That quite frankly, is not acceptable. And as I have expressed to you privately, prior to proceedings here today, we do not on these benches, therefore, believe that you can continue in your role as Speaker.
"We do not have confidence in your ability to do so. So I would therefore welcome clarity, either from yourself, or indeed from the Leader of the House [Penny Mordaunt], as to how we can best facilitate a vote in this chamber at the earliest possible occasion to that effect."
Responding, the Speaker apologised again and said the decision had been taken because of threats tp MPs. He offered the SNP the chance of an emergency debate on his position.
“I will reiterate I made a judgement call that didn’t end up in the position where I expected it to.
“I regret it. I apologise to the SNP… I apologise and I apologise to the House. I made a mistake. We do make mistakes. I own up to mine."
He added: “I will defend every Member in this House. Every Member matters to me in this House.”
“And it has been said, both sides, I never ever want to go through a situation where I pick up a phone to find a friend, of whatever side, has been murdered by terrorists.”
Sir Lindsay continued: “I also don’t want another attack on this House. I was in the chair on that day.
“I have seen, I have witnessed, I won’t share the details, but the details of the things that have been brought to me are absolutely frightening on all members of this House, on all sides.
“I have a duty of care, and I say that, and if my mistake is looking after Members I am guilty.”
Sir Lindsay added: “I am guilty because… I have a duty of care that I will carry out to protect people.
“It is the protection that led me to make a wrong decision but what I do not apologise (for) is the risk that has been put on all Members at the moment. I had serious meetings yesterday with the police on the issues and threats to politicians for us heading to an election.
“I do not want anything to happen again. So yes, I will apologise, I always will when I make a mistake...But I will also say I will do whatever it is to protect anybody in this chamber or anybody who work in this House. That is my duty of care.”
Earlier, Ms Mordaunt told MPs the chamber must “never bow to extremists, threats, or intimidation.”
She added: “It has not, it will not, it must not.
“And I would ask all honourable members not to do this House a further disservice by suggesting that the shameful events that took place yesterday were anything other than party politics on behalf of the Labour Party.”
READ MORE: Poll: Should Lindsay Hoyle step down as speaker of the House?
At Holyrood, Mr Yousaf took told journalists: “(Sir Lindsay’s) position looks to me to be untenable.
“What we saw was frankly disgraceful, chaotic scenes in the House of Commons.
“I think the true tragedy of that is that it takes away from what is the most important issue, and that is the fact that we have an absolute humanitarian catastrophe that has unfolded and is deepening in Gaza.”
The SNP leader said his party has been consistent in its approach to the Israel-Hamas war, and he continues to have family in Gaza who he said are “suffering”.
He added: “I don’t think it’s unreasonable for an opposition party on opposition day to want to have their motion debated, discussed and voted on.
“We know the Speaker looks like he has bent the rules and he has serious questions to answer.”
Meanwhile, Scottish Conservative leader Mr Ross said the Speaker has “an awful lot of work to do” to rebuild the confidence of MPs.
Downing Street repeatedly refused to say whether Rishi Sunak has confidence in the Commons Speaker.
Asked whether the Prime Minister has confidence in Sir Lindsay Hoyle, Mr Sunak’s official spokesman said: “The Prime Minister’s focus is on addressing the situation in the Middle East.
“And as I say, that is what he’s spending his time focused on. Matters for the House, as I say, are matters for the House.”
Number 10 said it was “entirely reasonable” for the Government’s position to be set out when asked if it regretted tabling a motion.
There is no easy mechanism for removing a Speaker, but more than 60 MPs have now signed an early day motion expressing a lack of confidence in Sir Lindsay.
A similar process was used to oust Michael Martin in 2009.
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