Woodland owners have expressed concern over a decision by the Department of Agriculture to allow certain plants to be imported as material for hedges on Irish farms.
As part of the new Agri-Climate Rural Environment (ACRES) scheme farmers are to be paid to plant more trees.
Up to 2,000km of new hedges are expected to be planted under the first Trance of the scheme.
The deadline for planting to be completed is the end of March next year.
It was planned that only plants of Irish origin would be used for planting.
Whitethorn is one of the most commonly used plants for farm hedging in Ireland.
But now there is a shortage of whitethorn plants to meet the demand.
Max Gullo has a nursery in Ballyneety in County Limerick and grows Irish Whitethorn.
He said that he has been inundated with calls from farmers seeking hedging plants. He said that he had thousands of plants and now has only a few hundred left.
"Nurseries like mine had no forewarning of the demands of this scheme.
"It takes 3 years to grow whitethorn from seed and it's impossible to provide the numbers of plants that are required.
"I don’t think plants of Irish origin can be sourced in Ireland now at the numbers required".
The shortage has led to the Department of Agriculture to allow plants that have been imported to be used for whitethorn hedging.
This has raised fears of the possibility of a new disease being inadvertently imported.
Simon White is Chairman of the Limerick and Tipperary Woodland Owners group. He is one of over 6,000 farmers who has seen his Ash trees decimated by the Ashdieback disease.
He said it is "ridiculous" that plants will now have to be imported to meet the requirements of a Department of Agriculture scheme.
"If you import material, you import risk.
"We have seen this with Ashdieback. The Ash trees were certified, but it didn’t stop the disease coming in.
"Now woodland owners have lost thousands because of this disease that was imported".
He added, "this risk could be avoided if only the Department had made sure that the plant material- of Irish origin- would be available for farmers.
"There should have been dialogue with nurseries 3 or 4 years ago to make sure the plants were grown".
Catherine Keena is Countryside Management Specialist with Teagasc.
She said that this situation underlines again the need to invest in our plant nursery industries that are growing plants from Irish seeds.
"From a biodiversity and disease point of view it’s important that we use plants that have been grown on this island which are in tune with associated native fauna.
"When you are importing plants, you are running the risk of importing something else, be it bugs or a disease and that is something we need to avoid. We need to build up our own nursery industry to avoid any of these risks."