THE Scottish Government will miss the deadline for paying EU farm subsidies for the second year in a row because of a botched £178 million IT system, it has been confirmed.

Rural Economy Secretary Fergus Ewing said officials expected to process around 90 per cent of payments before Friday, falling short of the EU’s 95.2 per cent target.

He also told Holyrood’s rural committee ministers had applied to the European Commission for an extension to October 15 to make the payments, but had yet to hear back.

He said the letter was sent last Wednesday - the same day he failed to mention it in a Holyrood debate and the day before Nicola Sturgeon ducked direct questions about an extension at First Minister’s Questions, leading to claims of a cover-up.

"If the criticism is I didn't mention things... in a political debate about a letter that was sent out the same day, I think we are moving into somewhat fanciful territory," he told the committee.

The SNP government was fined £5m by Brussels last year for failing to process Common Agricultural Policy (CAP) payments for 2015 on time, and now faces further fines for 2016.

Audit Scotland has suggested penalties could hit £60m, although Mr Ewing disputes this.

Pressed on whether his department would meet the June 30 deadline for this year, Mr Ewing said: “Our central forecast is we will make around 90 per cent of payments - in other words we will fall short by a few percentage points.

"We expect that virtually all the eligible payments will be made by August 30."

He said it was not possible to guarantee what payments would be made by the end of week “because of the complex interactions between IT functionality, the validation of claims... and the processing of payments by our offices across Scotland”.

He said a contingency system of loans for farmers and crofters affected by delays would be used if required, as it was last year.

He also told MSPs 25 of the 20,000 CAP payments from 2015 remained outstanding.

He refused to release a secret report on problems with the government’s CAP payment IT system, as he had been advised there were “potential threats to cyber security” in doing so.

LibDem MSP Mike Rumbles accused Mr Ewing of hiding behind security, and claimed the report had been buried because its contents were so politically embarrassing.

He said: “Fergus Ewing confirmed he has presided over CAP shambles 2.0, once again letting down farmers who are in need of vital funds.

“He is completely oblivious to the disarray in our agricultural sector and that our rural economy has taken damaging hit after damaging hit.

“It has been almost two years since this debacle began and there is no end in sight.”

Labour’s Rhoda Grant said: “The SNP’s handling of the CAP payments fiasco has descended into farce and secrecy yet again.

“Fergus Ewing has confirmed ministers were told about his intention to beg Brussels for an extension to deadlines, only for him and Nicola Sturgeon to later plead ignorance to MSPs.

“This dishonesty has done nothing but add insult to injury. Farmers and crofters have faced foul-up after foul-up – and SNP minister Fergus Ewing has now lost their confidence.”

Tory Peter Chapman said: “This is yet another incident of the SNP completely lacking in transparency. It’s insulting to the parliament and, more seriously, a slap in the face to thousands of farmers who are yet again waiting for crucial CAP payments.”