The Country Land and Business Association (CLA) have issued a statement following a report by the Public Accounts Committee.
The report was made in the light of the 2015 Common Agricultural Policy (CAP) payments.
CLA president Ross Murray believes that lessons need to be learnt from the error, and a clear, workable system should be put in place.
Mr Murray said: "It is vital that we have learnt the lessons from the challenges of 2015 and 2016 to ensure an effective, clear and workable system is in place in the future.
"A combination of a rushed and failed digital experiment, poor initial communication and a flooding crisis meant some farmers were forced to borrow money or sell livestock or machinery in order to keep their heads above water.
"We have seen positive steps taken by the RPA in administering this year's round of CAP payments but it is clear a better understanding of the risks involved in late payments on farm businesses is needed.
"Any uncertainty, confusion or delay is unlikely to encourage much needed investment.
"Establishing a simpler, more transparent, payments system should be one of the main objectives of a new post Brexit policy that supports farmers and land management."