The Scottish government is expected to process around 90 per cent of CAP payments, falling short of the EU's 95.2 per cent target.
This will mean they will miss the deadline for paying EU farm subsidies for the second year in a row because of the botched £178 million IT system.
Scotland's rural secretary Fergus Ewing faced questions from MSPs yesterday (28 June) over delays to the distribution of EU farm subsidies to farmers.
Mr Ewing sought to calm tensions at the rural, economy and connectivity committee on how work to distribute Common Agricultural Policy (CAP) payments is progressing.
He insisted that the 'vast majority' of Scotland's crofters and farmers have received the payments.
The committee heard that First Minister Nicola Sturgeon's letter, which pleaded for an extension to the deadline, has not yet been confirmed by the European Commission.
The letter was sent last Wednesday.
Mr Ewing also explained to the committee that 25 of the 20,000 CAP payments from 2015 remained outstanding.
'Flogging a dead horse'
Last year saw problems in the Scottish government's IT system which caused delays prompting the government to ask for an extension to October.
A 'highly critical' report into the £178m IT system has created a rift between MSPs and Mr Ewing.
Farming leaders have previously asked whether the government is "flogging a dead horse" by sticking with its IT system for delivering CAP support.
Farming union NFU Scotland said every farmer will remember 2016 as a year when the Scottish government's 'flawed IT system failed to deliver' the subsidy CAP payments, 'damaging' the rural economy.
Former President of NFU Scotland Bowie said: "The level of frustration and lack of trust in Scottish Government's ability to properly deliver payments across all schemes in a timely manner remains unprecedented."
