As widely, expected Rural Affairs Secretary Richard Lochhead has agreed to extend the Single Application Form (SAF) window by a month until June 15.
However, the Scottish Government is to stick to its preference for online submissions, despite the IT system being beset with problems.
Meanwhile, technical experts would continue to attempt to improve the online system and would react to issues as they arose.
Mr Lochhead also pledged the Scottish Government would make “every effort” to stick to the payment schedule.
“Delivery of the new CAP is an absolute priority for the Scottish Government. The system is complex and has presented significant challenges in Scotland and across Europe, as shown by Commissioner Hogan’s announcement that a four-week extension to the application window would be allowed,” he said.
“Having carefully considered all of the options, consulted widely and taking into account the hard work going on behind the scenes to maximise the performance of our online system I have decided to extend the Scottish application window by a month until June 15, subject to the approval of EU legislation which is expected next week.
“As part of our efforts to make payments as soon as possible we will look at all flexibilities permitted within the EU rules, and I strongly encourage the EU to give additional flexibility, particularly around the inspection regime which has already been called for by other member states.
“Of course, paper copies of the forms have always been and continue to be available to farmers and crofters.
“We will also continue to respond to reports of issues with the IT system as quickly as we can, and liaise regularly with industry representatives to ensure views are taken on board every step of the way.”
This does not change the current closing date of the Agri-Environment Climate Scheme, which remains as June 12.
NFU Scotland has welcomed the extension.
Given ongoing difficulties being experienced by those accessing the new computerised application system, the NFUS believes the extension will allow more time for the forms to be completed electronically, with online submissions the preferred method.
NFU Scotland chief executive Scott Walker said: “With exactly a month to go until the original deadline date of May 15, it was clear from the calls and emails that we had received that some members were having difficulties using the new online application system and that a deadline extension made sense.
“We welcome Scottish Government efforts to quickly upgrade and improve the computer system as issues arise, but the deadline of 15 May was looming large.
“A month’s extension will now give the industry a cushion of comfort to make sure we get as many applications submitted electronically as possible.
“With the extension announced, we would urge farmers not to put the brakes on the application process and delay it until the last minute.
“This is a new scheme and a new application process, and claimants must make allowances on the time it may take to complete it successfully.
“The sooner they start, the earlier any problems will be identified and help can be sought.
“Extending the application period will justifiably raise concerns that the traditional December payment window for support payments will be missed. We have asked Scottish Government to be straight with Scottish farmers and, if payment delays are likely, then we have asked that they give producers early notice so that business planning and any necessary arrangements can be put in place.
“We have already raised with the EU Commission the possibility, if systems fail, of making a part payment within the normal December window.
“The difficulties being experienced across Europe in introducing the new CAP shows that we are not alone, and the option to make part payment would recognise these exceptional circumstances.