Scotland’s taxpayers are facing £125 million of EU fines thanks to a litany of mistakes and incompetence by the SNP government that meant hundreds of millions of pounds of support were not paid on time to farmers, according to a damning official report.

An Audit Scotland study into the shambles surrounding the creation of a new computer system to make payments under the Common Agricultural Policy (CAP) said the Scottish Government is now admitting there is an “extreme risk” all the money will not be paid June 30.

If this deadline is not met, the report said the Scottish taxpayer is liable for European fines of between £40 million and £125 million. This is in addition to the cost of the botched computer system itself, which has increased 74 per cent to £178 million.

The report said that in December 2014 a whistle-blower made Scottish ministers aware that the “delivery director” responsible for delivering the programme at the minimum possible cost owned an agency that provided dozens of staff.

Although this was a clear conflict of interest, he was allowed to continue to signing off overtime claims for staff employed by his agency and it took eight months for the Scottish Government to include the conflict on an official register.