The European Commission has said it cannot give farmers 14 days notice of inspection of feed and food law, animal health and welfare and identification and registration of animals.
Farmers here had been seeking to have the regulations changed to allow all inspections of farms to be notified to them because so many farmers now work part time.
However, the commission, which had been asked to examine the whole area of compliance with EU rules, said it would create the possibility to give notice of checks up to 14 days in advance as long as the purpose of the controls was not jeopardised.
"National authorities will be required to identify the optimal time of year to check most of the obligations, while ensuring that no obligation is ignored in the control system," the commission report issued at the weekend noted.
Minister for Agriculture Mary Coughlan is this week meeting the farm organisations to determine how to proceed with the inspection regime. She has been coming under increasing pressure inspections and penalties imposed for breaches of the EU rules.
Farm organisations have said the rules are too complicated and the levels of penalty imposed for minor breaches are far too high.
Ms Coughlan had lobbied her European counterparts to seek an easing of the cross-compliance rules with some success and the matter had been referred to the commission for a report.
This report moved some way to meeting the demands of farmers not just here but in Germany and France, where similar objections had been put forward.
Mariann Fischer Boel, commissioner for agriculture and rural development, said cross-compliance was a central part of the reformed Common Agricultural Policy.
"Direct payments will only be acceptable to the public if people can see that our farmers are being rewarded for carrying out vital tasks in the countryside," she said. "I am well aware that many farmers are very unhappy with cross-compliance, but it is right and it is necessary and it is here to stay. However, this does not mean that we cannot make changes to make it work more effectively."
Improvements which the commission said should be looked at included allowing member states not to pursue cases of non-compliance which would not trigger the minimum reduction and to exempt penalties below €50.