As many as 10,000 farmers may not get paid their EU grants this year because they are not in the electronic pay system.
The EU has ended the cheque in the post system here and is insisting that this year the €1.4 billion to be paid out will be transferred electronically into an account number nominated by the farmer.
While the electronic financial transfer (EFT) system has worked well elsewhere in Europe, Irish farmers have been slow to come forward with account numbers into which their Single Farm Payments can be made.
Now, according to Derek Deane, deputy president of the Irish Farmers' Association, the decision to make EFT compulsory will lead to a significant number of farmers not getting paid.
Mr Deane said some farmers have greater trust in getting a cheque directly from the Department of Agriculture and then deciding where the money would be lodged.
"Many farmers deal solely with credit unions and An Post, who are not part of the electronic transfer system, and that is a very serious problem for them," he said.
Mr Deane said farmers as a right should have the option of whether they get paid directly into their bank or not. If this option is not given up to 10,000 farmers will not be paid in the normal way.
Discussions are continuing between the EU and An Post to include it in the new system. However, no discussions are taking place with the credit union movement.
Fewer than 50 per cent of Irish farmers had provided bank account numbers to the Department of Agriculture to make the electronic payments by the end of last year despite continuing pressure on them to do so.
The European Commission had told the Government it will no longer allow payment in cheques.
"This means that we cannot issue cheques to farmers and if we do so, the State will be penalised by the commission," said a department spokesman.