EU agricultural commissioner Phil Hogan has met with Scotland's First Minister to discuss the Scottish government's failures in handling the Common Agricultural Policy payments.
Scotland is facing a £125 million fine from the EU because of a series of mistakes led to farmers not being paid their support payments on time.
An Audit Scotland study into the computer system that was designed to make the payments under the Common Agricultural Policy warned the project is at risk of running out of money because of costs.
Mr Hogan discussed the issues with First Minister Nicola Sturgeon and her new rural economy secretary, Fergus Ewing, at Bute House in Edinburgh.
A spokeswoman for the Scottish government said: "It was a good discussion and the first minister and Mr Ewing found the meeting with the commissioner to be very positive."
Opposition parties said the spending watchdog's findings revealed a 'litany of failure' and 'incompetence.'
Audit Scotland said ministers were aware of the issue in the project to reform EU rural subsidies.
The Government admitted in March there is an 'extreme risk' it will not make all the required payments by the European Commission's (EC) deadline of 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.
"The scale of the challenge ahead should not be underestimated," said Caroline Gardner, Auditor General for Scotland.
"It’s vital that the Scottish Government take steps now to ensure the IT system is fit for purpose and fully assess the potential financial impact if it’s unable to meet the European Commission’s regulations within the programme’s remaining budget.
"The CAP Futures programme has been beset with difficulties from the start.
"These problems, and the way they have been dealt with by the Scottish Government, are a serious concern, particularly as the programme continues to face major obstacles and is unlikely to deliver value for money.
"There is a significant risk that the Scottish Government will not deliver its aim to minimise financial penalties charged by the EC for non-compliance with regulations. A range of financial penalties is possible, with a potential range between £40 million and £125 million, subject to an assessment of the specific circumstances by the EC."
