It is not possible to tell if documents relating to misconduct allegations against former first minister Alex Salmond have already been deleted from the Scottish Government’s computer system, Permanent Secretary Leslie Evans has revealed.

Scotland’s most senior civil servant told MSPs it is “not technically possible” to know what documents have been automatically wiped from the system.

Ms Evans added that if material has been deleted it was not possible for it to be retrieved.

With the Scottish Government computer system automatically deleting Outlook documents that have not been saved on to the corporate record after 14 months, the Permanent Secretary had already stepped in to prevent this from happening with certain employees.

MSPs on the Holyrood committee set up to probe the Government’s handling of the allegations against the former SNP leader first raised concerns about the “preservation of evidence” at the end of March.

At the time Ms Evans told members of the Committee on the Scottish Government Handling of Harassment Complaints that she had “instructed the halting of the automated deletion of some users’ content”.

But with the Scottish Government computer systems set up to automatically delete items not saved to the corporate record after 14 months, the Liberal Democrats raised concerns that some relevant documents could already be lost.

MSP Alex Cole-Hamilton said: “Deleting electronic communications that are more than 14 months old when the inquiry is looking into a complaint made 15 months ago is deeply troubling.”

He added: “It will be far more difficult to complete a comprehensive probe that retains public trust when not all of the relevant documentation and correspondence is available.”

He spoke out after Ms Evans said the steps that had been taken “ensure that for the specified users any such material which was created before the instruction was given and which ordinarily have been deleted at the 14-month point has instead been preserved”.

She added that for this group of employees “all such future material will also be preserved for these system users”.

Committee convener Linda Fabiani raised concerns about the ‘preservation of evidence’ in March (Andrew Milligan/PA)

Ms Evans, in response to a letter from committee convener Linda Fabiani, stated: “You asked whether documents which may be relevant to the committee’s inquiry were deleted before the instruction was given and what steps are being taken to recover this information.

“It is not possible technically to tell what has been automatically deleted or to retrieve material which has already been deleted from the system.

“However the automated deletion process applies only to Outlook material which has not been stored as part of the corporate record and in electronic filing systems, and written guidance to staff makes clear the information, governance standards and procedures which apply to all Scottish Government business.”

The committee was set up to look at the matter after a court ruling in January that the Scottish Government’s handling of sexual misconduct allegations against the former first minster was “unlawful”.

He had raised a legal challenge to the process, taking this to the Court of Session in Edinburgh, after it emerged the investigating officer had had  previous contact with the two women who made the allegations.

Following that ruling in January, Ms Evans pledged that an internal review of procedures within the Scottish Government would be carried out.

A separate investigation is also taking place to determine if Ms Sturgeon breached the ministerial code in meetings and conversations with the former first minister before the court case.

MSPs on the committee have already agreed their investigations are to be put on hold until the conclusion of a court case against the former SNP leader.

He has been charged with 14 offences, including two of attempted rape, and denies “absolutely these allegations of criminality”.

A Scottish Government spokesman said: “Our Corporate Records Management Plan makes it absolutely clear to staff that material of importance must be stored to the corporate record which, since 2005, has been our electronic records and document management system.

“It’s important to note that material saved to the corporate record is absolutely not subject to automated deletion after 14 months and is retained in accordance with the retention and disposal schedules outlined in our Corporate Records Management Plan. The Records Management Plan is fully compliant with the Public Records (Scotland) Act 2011.

“Automated deletion occurs only to items held in Outlook mailboxes which have not been saved to the corporate record. The archival and deletion process for Outlook content has been in place since 2008 and is standard industry practice in relation to digital information.”