In recent weeks, batches of farmers have been sent letters asking for money from their 2005 and 2006 entitlements to be repaid.
The RPA admitted last year that 20,000 entitlements under the 2005 and 2006 were calculated incorrectly.
Overpayments to farmers in those two years totalled £37m, the RPA said, though many farmers were unaware they had been paid too much money.
Several farmers have contacted Farmers Weekly over the letters from the organisation, which state they had to repay money within 30 days.
Some had been told they had to repay substantial amounts of their entitlements from those years.
Ken Hayter, who farms 29ha (72 acres) in Wimborne, Dorset, said he was told almost a third of his 2005/2006 single payment had to be repaid.
“As far as I know I have not made any mistakes or claimed too much money.
“I tried to speak to the RPA, but I was told they had just decided they had overpaid.
“They have devised a system that’s so complicated they can’t get it right and its costing the farming industry money.”
Michael Barnes, who runs a 53ha (130-acre) livestock farm in Malvern, Worcestershire, claimed he was given no reason by the RPA over why he should repay £400 from his £6000 payment.
“If I have made a mistake I would repay the money, but I rang the RPA and was told they weren’t allowed to say what the mistakes are.”
Mr Barnes said the letter from the RPA said the money should be repaid within one month or interest charges would be applied.
“I am only a small producer, but it’s a substantial amount to my business,” he said.
NFU policy adviser Richard Wordsworth said the RPA’s timing “wasn’t great”, particularly as most farmers in England had not yet received their 2008 single payment.
Mr Wordsworth said the letters failed to explain to claimants exactly why the RPA thought they had been overpaid, showing that a lack of communication between the RPA and farmers was still an issue.
“It concerns me that those letters will have a personal and business impact, but no background information is provided,” he said.
“It feels a bit like a person in the street asking for money. What farmers need is the background information on how the RPA gets to that figure.
“They need to contact the Customer Service centre and ask for the figures to be provided.”
An RPA spokeswoman said the agency had been contacting customers about SPS overpayments for many months now.
“Inevitably there is a greater focus on claim validation at this time of year and so we will be continuing to contact customers as we identify discrepancies in their claims.
“The causes of these overpayments, include partial payments in 2005 and 2006 (where the final claim value is now less than the amount due); penalties and entitlement correction work that customers asked us to carry out.
“The main reason for the overpayment is outlined in the letter and we enclose an invoice for the scheme year or years, where there has been an overpayment.”
The spokeswoman added that the agency was aware that repayment could cause inconvenience and so it was offering customers a number of ways in which they can repay, including a monthly payment plan to complete the repayment within 6 months.
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