A 10ha limit will be imposed on the amount of land that a farmer can put into species-rich grassland and traditional hay meadows in this year's AEOS scheme.
The new maximum is one of several changes from the scheme launched last year.
For this year, farmers who have applied for a nitrates derogation on their land will not be allowed to claim payment in the species-rich grassland, traditional hay meadow, riparian margins, arable margins or establishment and maintenance of habitats measures.
It is understood that some payments to around 100 derogation farmers in last year's scheme are now under scrutiny by Department of Agriculture officials, even though agricultural consultants maintain this was not made clear in the terms and conditions last year.
Other farmers have fallen foul of the rule that they can only claim one measure per land parcel. For example, a farmer who planted a new hedgerow along the edge of a traditional hay meadow needed to divide the land into two separate parcels to get paid on both measures.
Other changes to this year's scheme include the requirement for a soil sample from the farm. Soil samples will only be required after a farmer has been approved for entry into the scheme and must be supplied before March 31, 2012.
Meanwhile, the Department is to start inspections on 5pc of the farms that were approved for the AEOS scheme last year. Around 400-450 farms will be inspected in the coming weeks.
It is understood that payments will be issued to farmers once on-farm inspections have been completed and approved by the Department of Agriculture.