The Irish Farmer's Association believe IT issues have affected the rollout of the scheme.
The IFA is calling for an extension to the Shannon Callows Flood Scheme, after applications closed on Monday night.
There are claims that IT issues have meant that some farmers to not yet receive their expression of Interest forms or been contacted by the Department of Agriculture.
Flooding along the Shannon during the summer, which caused damage to farms in the area.
IFA Presidential Candidate, and beef and sheep farmer from Ballinakill, Francie Gorman says not all lands that were flooded have been identified by the system, leading to the delays in contact: