The NAO last week issued a third report into the Government's administration of the SPS.
It concludes that both the Rural Payments Agency (RPA) and Defra have shown scant regard for protecting public money in the way they have handled the scheme.
Additional administration costs and provisions for EU penalties have amounted to more than £580m since 2005.
NFU President Peter Kendall said: "I've said it before and I'll say it again. This is down to Defra's rushing to implement — despite warnings about the risk — a hugely complex model of single payment on purely ideological grounds and with no regard for the consequences. Initially, it was farmers who paid the price, but now it is taxpayers who are picking up the tab for the whole sorry mess."
Commenting on the NAO's finding that the average cost per claim was £1,743 in England versus a cost of £285 per claim under the simpler Scottish system, Kendall said: "The difference in the cost of processing a claim in England and Scotland says it all. It is a shameful example of what ill-thought-out policy-making can mean.
"The key issue now is for the Government to find a way out of this mess. That will take an honest assessment of what is actually doable and what is simply beyond the capacity of the system. Whatever the outcome, the lesson for any future CAP implementation is clear; policymakers must pay heed to implementation issues — they are part and parcel of policy."
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