About 14,600 farmers is Scotland will receive a share of £12.2m which had been set aside from 2013 CAP payments as part of EU budget balancing.
The Scottish government was required by the EU to keep the funds back for an emergency fund, which resulted in 14,600 farmers who would have received 2013 SFP payments of more than €2,000 having theirs cut by 2.5%.
The Commission is now allowing the payment of unspent reserves and those who had money held back will receive an averaging of £845 each.
The Scottish government says it has started repaying the money and funds will start to appear in bank accounts from 11 June.
Richard Lochhead, the rural affairs secretary said:
“This will be a modest albeit welcome windfall for thousands of Scottish farmers and crofters who had their payments reduced in 2013 as required by Europe.
“Of course, the level of financial discipline imposed by Europe in 2013 would have been millions of pounds higher had it not been for the Scottish Government successfully lobbying the EU to minimise the impact on Scottish agriculture.
“It is also a timely reminder for farmers and crofters to submit their Single Application Forms (SAF) for 2015 CAP support as soon as possible.”
The Scottish government has now received 11,677 SAFs – more than 50% of the expected final tally.
There is less than two weeks until the June 15 deadline.