The Scottish government must pay back £35m in EU money to Brussels for errors in its single farm payment system.
The fine has been imposed by the European Commission following an audit of the single farm payment scheme (SPS) in 2009.
Although the fine relates to the accuracy of the land maps used by farmers as part of their annual support claims, there will be no impact at farm level of this disallowance.
NFU Scotland said the main problem with farm payments identified by the audit related to the inclusion of ineligible areas not identified at inspection, the accuracy of the information held on Scottish government systems regarding field boundaries and the location and extent of ineligible features.
The union said it believed the current CAP reform negotiations offered the opportunity to identify a better mapping system and therefore it has opened discussions with Brussels.
NFU Scotland president, Nigel Miller, said: "No fine is ever good news, but a key point for farmers to keep in mind is that this announcement will have no impact on their payments and is pitched at a national level. "This episode does underline the necessity of the action we took in 2010, alerting members to the importance of proactively re-mapping their land area when submitting support claim forms to ensure that only eligible areas were included."
"The improvements applicants undertook at that time and on subsequent claim forms will have helped to ease the problems being encountered when farms are subject to official inspections. The irony and unintentional consequence is that several of those who have been responsible and made changes to their maps have since found themselves subject to delays when receiving payments."
He added: "The planned changes to support schemes and CAP reform provides an opportunity to correct this issue and to ensure a pragmatic and realistic level of accuracy on mapping and land eligibility is a feature of any future support claim forms."