The Rural Payments Agency says it is investigating 13,000 Basic Payment Scheme claims from farmers who believe they have been underpaid.
The RPA said it was writing to all claimants whose payments are part of its planned “payment reconsiliation process” to let them know what is happening and what they can expect.
RPA chief executive Mark Grimshaw said: “We are now focused on looking at 2015 payments where there’s a difference between the information on the claim and the information we hold.”
This would ensure each farmer was paid everything they were eligible for.
The RPA will start writing to claimants by the end of June.
Mr Grimshaw said the process would initially look at around 13,000 individual 2015 BPS claims, many of whom wrote to RPA.
It would investigate any differences in land and entitlements held and making any necessary data adjustments and top-up payments.
The process will see the RPA focus on getting as much money paid to farmers as quickly as possible by looking at those claims with the biggest payment difference first.
It will contact the farmer or agent if the RPA needs more information. Once the work is finished, each farmer or agent will be informed of the outcome.
A claim statement will be issued and the RPA will explain to the farmer what they have done, when any additional amount is paid.
Mr Grimshaw said the agency would also update the data it will use to check the 2016 claim when it adjusts a farmer’s 2015 claim information.
“The past year has been about building the foundations of the new Rural Payments service, which will reduce fines for the UK and mean quicker and compliant payments for farmers.
“We have all the resources we need and expect 2016 to be easier for our farmers. It has already got off to a good start with a record 80% of claims submitted online.”
As of 26 June, 86,678, (99.5%) farmers have received a payment on their 2015 BPS claim. Anyone with a query can still write to RPA, so it can investigate.