The Rural Payments Agency (RPA) has seen a significant increase in the volume of complaints recorded, according to government statistics.
Queries raised by farmers over their BPS payments under the 2015 scheme were raised as complaints in 2016-17.
The agency conducted a standard reconciliation of BPS 2015 payments and as these were completed associated complaints were able to be resolved.
At the end of March 2017 just over 2,000 complaints were unresolved.
The RPA has recently refined its complaints process, to take on feedback from farmers, agents and stakeholders, who felt that the previous process often took too long for complainants to get through.
However, only 25 appeals against decisions by the RPA were received in 2016-17. This was the lowest number of appeals received for more than ten years.
