Farmers across the Northern Sound region face paying back a combined €351,500 in BEAM payments.
The scheme required farmers to reduce bovine organic nitrogen produced on the farm by five percent, over two years.
However, hundreds of farmers were unable to meet this commitment.
268 farmers across the region decided not to opt for a later reduction period and, as of the end of June, failed to meet this requirement.
In a majority of cases, farmers in the recoupment situation increased their nitrates during the reduction period.
Speaking in the Dáil last week, local TD Matt Carthy says the commitment to reduce bovine organic nitrogen caused "difficulty with the scheme from the outset".
Junior Minister for Agriculture, Martin Heydon, replied that "money is never given without some conditionality attached" and added "there has to be recoupment" if these conditions are not met.
130 farmers in Cavan will be expected to pay back a combined €158,000, while 138 Monaghan farmers owe a combined €193,500.
Deputy Carthy called on the Department to "make contact with the European Commission to find flexibility to allow those farmers were not fully aware of the proposition" and to seek an extension on the repayments.