The CLA called for ‘immediate action’ from Defra to address the continuing payment issues, outlining a four-point action plan to help resolve the current crisis.
It came as Scotland’s new Rural Economy Secretary Fergus Ewing vowed to make resolving the payments debacle his top priority.
Addressing farmers at this week’s Scot Sheep event, he apologised for failures in the Scottish Government’s roll out of BPS.
In a statement to Parliament, Mr Ewing said: “From day one in the job and for the foreseeable future, the resolution of Common Agricultural Policy [CAP] payment issues are my top priority.
“I want to assure those in rural communities I will devote all necessary time and attention to this task. It is my number one priority.”
NFU Cymru this week wrote to Secretary of State Liz Truss pressing Westminster for immediate payments for the hundreds of farmers on the Wales-English border still awaiting their settlements.
Stephen James, president of NFU Cymru said it was ‘extremely concerning’ that, in an age where it was commonplace for data to be easily shared between systems, information could not be ‘promptly and effectively shared’ between the RPA and Rural Payments Wales (RPW).
He said: “Businesses are being unfairly penalised by the delays just because their land straddles the Wales-England border and RPW and the RPA are unable to cope with the established situation.”
CLA president Ross Murray added: “Now the window for claiming or amending applications for 2016 payments is closed, Government must act swiftly to put an end to 2015 payment delays but also make longer term commitments to farmers to resolve these ongoing issues.
“We must remind Defra that much of the expenditure incurred by farmers in 2015 was in fact incurred from as long ago as autumn 2014.”
A spokesperson from the RPA said: "Our efforts are now fully focused on paying the remaining more complex claims, such as cross-border cases, which are harder than we anticipated.
"RPA introduced bridging payments to provide some financial relief while we complete processing on claims. We anticipate that we will complete this by the end of June.
"We work closely with farming organisations and welcome their insight. It will be valuable to add to our own learning as we move through BPS 2016 processing and payments into 2017."
Farmers in England have been urged to apply for the 2016 BPS before midnight on June 10.
A 1 per cent penalty is added for every working day the application is received after the initial deadline of May 16.