Humza Yousaf has given the clearest indication yet that the Scottish Government has lost evidence that could have been handed over to the UK Covid Inquiry – insisting that WhatsApp “messages that have been retained” will be submitted.

The First Minister was accused of “losing control” of his government after admitting he does not know which former and current Holyrood ministers have or have not deleted WhatsApp messages instead of handing over evidence in full to the inquiry.

Questions are hanging over former first minister Nicola Sturgeon, who repeatedly refused to say whether she has deleted WhatsApp messages exchanged during her time leading the Scottish Government’s pandemic response, despite claiming she has “nothing to hide”.

Read more: Nicola Sturgeon under more pressure over deleted WhatsApps

Deputy First Minister Shona Robison told MSPs on Tuesday that 14,000 WhatsApp messages, contained in group chats including at least three people and one a civil servant, will be sent to the UK Covid Inquiry by November 6.

But in the period between the first confirmed Scottish case of Covid-19 on March 1, 2020 and end date of inquiry's terms of reference on June 6, 2022, that would equate to only around 16 messages per day – raising speculation that a flurry of correspondence has potentially been lost.

It later emerged that the 14,000 WhatsApps messages mentioned by Mr Yousaf referred only to the Scottish Government’s “corporate” submission.

This involves 137 Covid-related WhatsApp groups of three or more people at least one of whom was a civil servant, and which may or may not have included a minister.

It excludes direct minister-to-minister messaging or messaging between just two people.

Submissions by individuals, including those by the First Minister and his predecessor Nicola Sturgeon, fall under a different form of request from the Inquiry.

The First Minister’s official spokesman confirmed it had been Scottish Government “guidance” to delete old WhatsApp messages but Mr Yousaf had not done so.

His WhatsApps had been recovered from an old phone, he said.

Speaking at First Minister’s Questions, Mr Yousaf said that the messages that have been kept will be handed over the the inquiry authorities, but suggested that some correspondence has been lost.

He said: “I can give an unequivocal guarantee to those families who have been bereaved by Covid that the messages that we have retained will absolutely be handed over and handed over in full.

“As the First Minister, as the head of this government, I will, when submitting my statement, be handing over my messages in full and unredacted.”

Read more: SNP to submit WhatsApps but cannot say if messages have been deleted

Labour leader Anas Sarwar accused the First Minister of having “lost control of his government” after Mr Yousaf told MSPs that he did not know which ministers had or had not retained all of their WhatsApp messages from during the pandemic.

Mr Sarwar pressed the First Minister over why he thinks the Scottish Government should be "held to a lower standard than the Tories at Westminster", after the UK Government was forced into handing over unredacted messages to the inquiry.

The Labour leader said that Mr Yousaf gave “no equivocation, no caveats, no grey areas” when he had confirmed in June that his Government would hand over messages to the inquiry.

The Herald: Scottish Labour leader Anas SarwarScottish Labour leader Anas Sarwar (Image: PA)

He added: “We now know messages have been deleted.

“This is about the conduct of the Scottish Government, so can the First Minister tell us, of the 70 ministers and officials, how many have failed to comply with a do-not-destroy notice and how many have deleted messages?”

Mr Yousaf said it would be a “pretty serious breach” of the confidentiality of the inquiry to ask current and former ministers what they had supplied.

The First Minister added: “I don’t know, of course, what requests have gone to individual ministers.”

But evidence heard at a preliminary hearing of the UK Covid Inquiry revealed the Scottish Government stated that “extensive individual” requests for evidence “have been administered by the Scottish Government through its Covid Inquiry response team”, raising questions over exactly what Mr Yousaf’s administration is aware of.

Mr Sarwar said: “The First Minister has lost control of his government.

Read more: Covid Secrecy row as Jason Leitch deletes WhatsApp messages

“He doesn’t know how many ministers or officials have complied with the do not destroy notice.

“He doesn’t know how many have deleted messages.

“And he claims that the Government’s response to the inquiry is for individuals rather than his government.

“The First Minister promised this chamber he would ensure all material was handed to the inquiry in full.“

Scottish Conservative leader, Douglas Ross, said the “secretive approach” from the Scottish Government was treating families left bereaved by the virus “with contempt”.

Mr Ross hit out at an “auto-delete” policy he said had been introduced by the Scottish Government, labelling it “the digital equivalent of building a bonfire to torch the evidence”.

The Herald: Scottish Conservative leader Douglas RossScottish Conservative leader Douglas Ross (Image: PA)

He told MSPs: “This week it was reported Nicola Sturgeon has deleted her WhatsApp messages.

“We know destroying or withholding evidence from an inquiry is illegal.

“Does Humza Yousaf accept that if Nicola Sturgeon or any Government minister has destroyed WhatsApp messages relevant to the inquiry, they would be breaking the law?”

Mr Yousaf replied: “In terms of accountability and transparency, Nicola Sturgeon stood up day after day, virtually every single day, did 250 media briefings, 70 parliamentary statements.”

He described that as “full accountability, full transparency” from Ms Sturgeon during the pandemic.

The row over the messages was sparked last week when Jamie Dawson KC, counsel to the UK inquiry, said “no messages” from within the Scottish Government had yet been provided.

However now a legal notice has been given, the Holyrood Government is in the process of handing over messages.

Mr Yousaf said: “On top of those 14,000 messages, when I submit my final statement I will be handing over many messages, not just with Cabinet secretaries, not just with ministers, with UK Government ministers, with opposition politicians I communicated with across the chamber.

Read more: Reports suggest Sturgeon and Yousaf deleted WhatsApp Covid messages

“I will be doing so unredacted, because this Government believes in accountability.”

Separate public inquiries have been set up by the Scottish and UK governments to examine the response to Covid, and the First Minister said: “I can give an absolute commitment the Scottish Government will fully co-operate with both inquiries.”

But Mr Ross insisted: “We don’t know what the truth is because messages have been deleted. And they have been deleted because of a policy of the SNP Government.

“That policy means they can cherry-pick the information the inquiry sees. Discussions may have been destroyed by their auto-delete policy.

“Any uncomfortable information may be lost, never to see the light of day.”