WhatsApp messages sent by Scotland’s former first minister Nicola Sturgeon about the pandemic were manually deleted from her phone, according to a report.

The Sunday Mail reported that documents given to the UK Covid-19 Inquiry show she is among a number of senior Scottish Government figures who say their WhatsApp data no longer exists.

They include current First Minister Humza Yousaf and former deputy first minister John Swinney.

It comes after the UK inquiry’s legal team said it believes the “majority” of WhatsApp messages shared among Scottish Government officials during the pandemic “have not been retained”.

As part of the inquiry, key decision makers – including ministers, former ministers and senior civil servants – have been asked to disclose communications, including those through informal channels such as Meta-owned WhatsApp, Microsoft Teams or Signal.

Mr Yousaf ordered an investigation by Scotland’s Solicitor General after Jamie Dawson KC – the lead counsel in the Scotland module of the inquiry – told the hearing on Thursday that the Scottish Government has not yet handed over messages.

A spokesman for Ms Sturgeon said: “Nicola will continue to provide all information requested by the inquiry that she holds and will continue to co-operate fully with both the UK and Scottish Covid inquiries.

“She has recently submitted her third written statement to the UK inquiry, running to around 200 pages, and expects to give oral evidence again next year when she will answer all questions put to her.”

Commenting in relation to all the former Scottish Government ministers, including Ms Sturgeon, an SNP spokesman said: “There has never been any hesitation by former members of the Scottish Government to provide any and all information they hold, when appropriately and legally requested by the UK and Scottish inquiries, and they will continue to co-operate fully.

“It would not be appropriate to comment further.”

A Scottish Government spokesman said that, as Mr Yousaf has made clear, the Scottish Government is “wholly committed to co-operating fully with the Covid-19 inquiries. This includes providing any requested material that we hold.”

The spokesman added: “More than 13,000 documents from the official record have been sent to the UK inquiry from the Scottish Government, in addition to the corporate and personal statements requested. Providing the formal decision-making record has been our priority.

“The UK inquiry has subsequently asked for WhatsApp messages relating to logistics and day-to-day communication, which we are working to provide.

“Given the interest in this specific request from the UK Covid-19 Inquiry, subject to approval from the Parliamentary Bureau, the Deputy First Minister will seek to make a statement to parliament on the issue early next week.”

A note to the inquiry from Mr Dawson and its legal team, published on Thursday evening, said it understands the majority of messages may have been deleted.

First Minister’s QuestionsScotland’s First Minister Humza Yousaf has ordered an investigation (Jane Barlow/PA)

The note said: “Given the potential significance of any such material, and in order to provide a clearer statement of the position, the Scottish Government has been asked to provide a full update on its position and that of all relevant Scottish Government witnesses as regards to their use of WhatsApps and their current availability for disclosure.

“It is currently understood that although WhatsApps appear to have been used to send messages relating to and surrounding key decisions by some members of Scottish Government, the majority of the messages have not been retained by witnesses.”

The Scottish Government said that while it is not its culture to use WhatsApp for decision-making, its records management policy states clearly that government decisions, however they are made, should be recorded in the official record.

It previously said that reports on Friday suggesting one of the people who did not keep informal messages was Scotland’s national clinical director Professor Jason Leitch were incorrect.

Scottish Labour has written to the Permanent Secretary to the Scottish Government, John-Paul Marks, asking for an urgent update on the state of data retention in the Scottish Government.

Scottish Labour deputy leader Jackie Baillie said “These bombshell revelations call into question what the SNP government is trying to hide.

“Humza Yousaf said his government would co-operate fully with the Covid inquiries but this promise has been left in tatters.”

She added: “The Scottish Government must come clean about exactly what happened here, what information has been lost and whether their data retention policy has been breached.”