The system is so rigid that often when a rule is recognised as being over the top or inappropriate or sometimes unworkable, it either cannot be changed for technical reasons or will not be changed for fear of opening up other problems. Worse still, it is left because people are too busy dealing with other problems.
Right now we're in the thick of working out detailed rules on how to implement the new CAP.
Interpreting the political agreement is done by way of 'delegated acts' drafted by the Commission in consultation with member states and the European Parliament.
The most recent example we have of how the system can come back to bite the individual is the issue of land eligibility for the single farm payment.
Over 19,500 Irish farmers have received letters telling them there are problems with their land parcels.
While all of these farmers got a shock when they opened their post, it turns out that most have nothing to worry about, but that more than 2,000 farmers will have problems with payments next year.
At virtually every farmers meeting I attend I hear about worries and concerns about inspections. Often the farmers have never been inspected but dread the day they might because they have heard stories about how other farmers were affected.
We hear of older farmers who are equally terrified and who, without the help of their neighbours and farm organisations, and dare I say politicians, would not be able to deal with some of the paperwork. We're talking about real people with worries which we have to take account of.
This hidden fear among farm families prompted me to write to the president of the Court of Auditors asking that his officials be sensitive to the human factor in their audits.
I also wrote to the Minister for Agriculture, Simon Coveney, urging him to also ensure that his officials take account of the personal circumstances of farmers who are subject to inspection.
I've spoken to MEPs from across the EU about this and they all share my concerns. In Brittany there is alarm about the high rate of death by suicide among farmers.
And lest people see this as an attack on Department officials, I have found that in the main there is huge sensitivity and humanity in those who deal directly with farmers where situations require sensitivity.
But these officials are also under pressure from the EU auditors and watch anxiously for the time when their own work may be subject to scrutiny.
I regret to say that what usually happens is that the innocent who make a mistake get punished, while those who bend the rules for excessive gain rarely get caught, the horsemeat scandal being an example.
There have been no charges or prosecutions. Yet, a farmer who brings an animal into the factory a few days over 30 months is immediately penalised.
Yes we need scrutiny of how public money is spent, but let's not victimise genuine people for their mistakes and let rogues go scot-free.
And let's be very careful about rules we write and make them fit for purpose.
Mairead McGuinness is a Fine Gael MEP representing Ireland East.