Thousands of farmers yet to receive their 2015 Basic Payment might now have to wait until mid-October for their money.
It follows a decision by Brussels to extend the 2016 deadline for member states to make CAP payments to farmers from 30 June to 15 October.
Previously, countries faced a hefty penalty if payments were made later than June.
The “exceptional measure” is for this year only. A number of member states were currently experiencing difficulties trying to complete payments before the 30 June deadline, said EU farm commissioner Phil Hogan.
But Mr Hogan said payments must still be made as soon as possible.
He said the derogation must not be used as an excuse to slow down the rate of payments and urged paying agencies to prioritise the issuing of all outstanding payments.
About 3,000 farmers are believed to be waiting for the BPS payments in England.
NFU vice-president Guy Smith said it would be an “absolute disgrace” if the Rural Payments Agency delayed payments longer than necessary.
The Scottish government said it was doing all it could to pay farmers before 30 June.
But it admitted that it was one of the countries that had asked the European Commission for flexibility.
Payment progress continues to be slow, with 86% of 2015 payments now made to 15,600 farmers with a total value of £204m.
The figures mean that since 25 May, the government has paid fewer than 400 additional farmers.
A government spokesman said the potential for flexibility on the deadline was discussed by Mr Hogan during a recent meeting with Scotland’s first minister, Nicola Sturgeon, and rural affairs secretary, Fergus Ewing.
NFU Scotland chief executive Scott Walker said the shift in the deadline for making payments was good news for the Scottish taxpayer.
But he warned: “Any deadline shift must not be used as an excuse by the Scottish government to delay the payment of outstanding 2015 monies any further or hold back progress with the 2016 scheme.”