Flooding in the main tillage areas is posing a major threat to €60 million worth of main crop potatoes which farmers are unable to harvest because of rain.
Along the east coast, the poor weather has already prevented the sowing of winter wheat.
The wheat crop is expected to be cut by two-thirds to only 30,000 hectares, farming experts said yesterday.
Mr Tom Maher, Teagasc's potato expert, estimated that 60 per cent of the main crop, Rooster and Kerr Pink varieties, were still in the ground.
"The potato stores are empty because farmers have been unable to dig potatoes for the past 10 days," he said.
"I was up in Meath on Thursday and I saw many fields under water and this was before the deluge. There are going to be heavy losses there," he said.
Mr Maher said that, apart from the potential loss by rotting, the main threat to the potato crop was now from frost, if the weather turns dry.
"Because of the amount of moisture in the ground, if there is frost, the crop will be totally destroyed," he said.
"As of now, potato farmers need 10 dry days to get the crop out of the ground and that will take us into December, leaving this the latest harvest ever," he said.
Mr Malachy Mitchell, national potato marketing co-ordinator and secretary of the Irish Farmers' Association National Potato Committee, said the harvest was at a critical stage.
"All this damage is coming at the end of what has been a poor year with reduced yields. It is critical," he said.
He said the wholesale price of potatoes had already increased by €20 to €30 per tonne and he hoped that this would not be passed on to the consumer.
"There is enough of a profit margin at that level without passing it on into the retail sector," he said.
Mr Jim O'Mahoney, Teagasc's chief tillage adviser, said many cereal farmers had been unable to plant winter wheat this year because of the condition of the ground because of waterlogging.
"It had been expected that 90,000 hectares would have been put in the ground this winter but to date only 30,000 hectares have been planted and we are almost out of time to allow any more planting," he said.
He said Meath, Dublin, Kildare and Louth had been very badly hit and it was unlikely that any more wheat would be planted.
"I am predicting that farmers will put their winter wheat crop land into set-aside or they may opt to plant less productive spring cereals, which must impact on the size of next year's grain harvest," he said.
The weather had also delayed the beet harvest but there were no major difficulties yet with the crop, he added.