As much as £35m may be lost if EU spending targets are not achieved, the finance minister informed the assembly on 13 December 2011.
During his statement on a recent North South Ministerial Meeting (NSMC), Sammy Wilson said the Special EU Programmes Body (SEUPB) had advised that if the current pace of commitment and spending continued, targets may not be met in 2013 and 2014.
He said the body "remained confident" that the INTERREG IVA cross border co-operation programme could achieve its 2011 and 2012 EU spending targets but could not guarantee the following two years following.
Finance committee chair, Conor Murphy, said he had "concerns" and questioned the minister on his specific measures to ensure the spending targets would be met.
Mr Wilson said he had been upfront with members about the risk and said SEUPB was working with officials in both jurisdictions to manage the identified risk in an attempt to ensure no funds were deducted.
The TUV's Jim Allister was critical of the SEUPB.
"This is bad planning, hopeless administration and poor oversight by the SEUPB, and yet it is one of the most handsomely funded bodies in these austere times," he said.
In his statement, Mr Wilson also said the SEUPB had advised the council that five local authority based groups under the INTERREG programme had approved 19 projects worth around £22m - a figure well short of their £50m expected share of the programme budget.
However, he said that local applications were currently under assessment.