Defra said last week the review would start shortly and last around six months. A panel will be looking at financial, operational and management activities.
Its chairman, director general of Defra's food and farming group Katrina Williams, will appoint an external contractor to handle the review. Part of its remit will be to look at the Single Payment Scheme (SPS).
Farming minister Jim Fitzpatrick said the review would ensure the agency was ready for the changes to the Common Agricultural Policy (CAP) due in 2013.
"It benefits us all to ensure the RPA operates efficiently," he said, adding that a key element was to "avoid deterioration" in the ability to make payments to farmers.
The NFU said "initial soundings" suggested that the check would assess future challenges rather than current performance, successes and failings.
NFU director of policy Martin Haworth said the review would help Defra ensure it was in a position to deliver CAP schemes efficiently.
"External input is vital, and the review board must not shrink from going back to the drawing board and asking fundamental questions about how CAP schemes are delivered on the ground and whether the RPA is the appropriate vehicle."
The RPA pays over £2bn of subsidies and environmental payments to farmers in England every year. But controversy dogs the agency.
Last March, growers said they were disillusioned with the way the RPA was running the Producer Organisation aid scheme because of endless paperwork.
Haworth said last week: "Defra must be prepared to make excellence in delivery a key measure of success. This means policy-making without adequate consideration of what can be delivered on the ground will become a thing of the past.
"We remain focused on the present performance of the RPA and are continuing to push for further improvements in SPS payment roll-out."
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