Farmers in England could be waiting for as much as £120m in 2015 Basic Payment Scheme support, according to calculations by the NFU.
The Rural Payments Agency announced on 1 May that all farmers had received either a full BPS payment or a bridging loan worth 50% of the value of their 2015 claim.
But six months after the opening of the payment window, the union has warned that it is “ridiculous” that thousands of farmers are still waiting for cash.
About 7,000 are understood to be waiting for the top-up payment to their bridging loan, while several thousand more believe they have been underpaid as a result of an RPA error and have lodged queries with the agency.
A number of the affected farmers are on cross border holdings, where payments are still outstanding because it has proved impossible to share data between the RPA and Rural Payments Wales.
Guy Smith, NFU vice-president, said the total BPS fund was about £1.43bn and the union estimated that the RPA had paid out in the region of £1.31bn.
“So there is a £120m deficit there and of that we think £60m is the second tranche of bridging payments and that leaves £60m, which we assume is underpayments.”
Under EU regulations, the payment window for BPS runs from 1 December to 30 June with interest paid on any money received by farmers after that date.
However, it has emerged that the EU Commission is currently considering extending this deadline until 15 October to give member states more time to pay.
Mr Smith said if this was the case, the NFU was adamant that farmers should be paid interest on any money paid after the end of June.
The Country Land and Business Association said the government needed to put an urgent action plan in place to address the ongoing issues.
The organisation has called for the RPA to contact individually any farmer yet to receive a payment to explain why not and to offer face-to-face meeting with claimants to speed up the resolution of outstanding issues.
It has also suggested contacting all claimants who have been subject to mapping changes to give them a chance to respond before any changes are finalised.
The reintroduction of dedicated case workers would also help support claimants, it added.
Daniel Kawczynski, MP for Shrewsbury and Atcham, said he had been approached by a number of farmers in his constituency to express their sheer frustration with the RPA.
“The vast majority of those I have spoken to have not received full payment but merely a partial one. This causes cashflow problems for the industry and needs rectifying quickly.”
An RPA spokesman said that over 81,800 (94%) of 2015 BPS claims had now been completed, but was unable to provide figures on the value of payments.
Ireland’s Ministry for Agriculture, Food and the Marine has already started preliminary checks on 2016 BPS applications and said it will contact farmers if they find any over claims, dual claims or overlaps.
Applicants will then be given the opportunity to rectify these issues online, with no penalty so long as it has been done by 20 June.
Member States have been given the option to introduce these preliminary checks as part of a CAP simplification agenda.
The Irish Farmers Association has welcomed the move saying it will reduce errors and speed up processing.