The Irish Farmers' Association has estimated that the bad weather of the past five weeks will cost farmers about €160m in extra animal feed and lost output.
The Minister for Agriculture Simon Coveney has said that his Department has applied to the European Commission to pay the Direct Farm Payment early this year.
Speaking on RTÉ's Today with Pat Kenny, Mr Coveney said that he was "reasonably confident" that the Commission would agree to make the payment on 16 October, instead of in December when it is due.
However, State farm body Teagasc says there could still be a good grain harvest if the weather improves over the next two weeks.
The IFA says that incomes have been hit in all sectors including dairy, beef, tillage and sheep.
It estimates that loss of output and higher animal feed costs will reach €100m.
Because of the problems in harvesting silage, farmers will have to buy extra feed over the winter costing an additional €60m.
IFA President John Bryan said only one third of the silage crop has been saved, which is very unusual at the beginning of July.
Teagasc is holding advice sessions for farmers at its nationwide network of offices tomorrow.
Teagasc tillage expert Jim O'Mahony said that the main tillage crops, winter wheat and spring barley, are standing up well to the weather, though there are problems with other crops.
Mr O'Mahony fears there could be more severe damage to crops if the bad weather continues.
But he said there could still be a good harvest if conditions improve soon.
