Almost two-thirds of farmers in England have received their 2008 single payment entitlement, despite continued complaints over the way claims are being handled.
About 70,000 farmers, or 65% of the total number of claimants, received their payments by 31 December, representing 59% of the total money available.
The RPA said it was working towards its target of making 75% of payments, by value, by the end of January.
Despite the progress, farmers have contacted Farmers Weekly over the way the RPA has dealt with applications.
Ian Robertson, of Green Farm, Norfolk, said he was concerned he could be waiting for months before he received his cheque, after RPA staff admitted they had lost his application form.
“All my neighbours had their cheques before Christmas, so I rang the RPA to find out where mine was.
“After first being told I hadn’t sent it in, I was then told it had been locked in a cupboard and they had no time to look for it.”
Mr Robertson said delays in receiving the cheque had left his 247ha (611-acre) arable business “up against it”.
“I have sent through another copy of the form, but it could take months for them to process. I’m left struggling through the RPA’s negligence.”
Meanwhile Peter Studley of Bickerton, Cheshire, said he was left with an £11,000 tax bill after the RPA overpaid him by £17,000.
“We didn’t know how much we should have been getting because we didn’t get a statement in 2005,” he said.
“By giving us that money we were pushed into the next tax bracket, leaving us with a tax bill of £11,000.
“Our accountant says we shouldn’t have to pay that now we know we were overpaid, but we haven’t got the £17,000 spare to pay back to the RPA.
“I wish I could earn a living without this rubbish.”
An RPA spokeswoman said the RPA would not comment on individual cases, but claims of lost forms would be investigated.