Farmers have raised concerns with the Welsh government after a Panorama investigation uncovered alleged illegal dumping of untreated sewage in Welsh rivers.
The ‘River pollution scandal’ aired on Monday 12 April and appeared to show untreated sewage being illegally discharged into protected rivers in England and Wales.
The BBC programme analysed data that showed some companies have regularly breached the conditions in their permits.
NFU Cymru has urged the Welsh government to carry out an investigation into the documentary's findings as it had caused 'great concern' among farmers.
The union called for reassurance that "agriculture has not been held accountable for the pollution caused from other sources, particularly sewage treatment works."
Farming groups in Wales have long highlighted that there are a range of factors influencing water quality in Wales.
John Davies, NFU Cymru president, said there was a 'false and flawed narrative' that framed agriculture as 'the problem' with respect to water quality issues.
“In light of the evidence uncovered by Panorama, NFU Cymru is seeking confirmation on what actions are being taken by government and the regulator to stop these illegal practices," he added.
"We also ask what investigations are being undertaken to understand if and where else within Wales similar illegal practices are or have taken place.”
As part of its letter, the union has also urged that any potential contribution that discharges are making to phosphate levels in the River Usk is accurately accounted for.
The River Usk was identified as having the highest level of phosphate failures of all Welsh Special Areas of Conservation (SAC) rivers.
Mr Davies continued: “We note that NRW analysis for the River Usk references agriculture but is silent on any potential contribution of the water companies to phosphate levels.
"It is important that the contribution of the water industry where through its permitted (or otherwise) activity is now properly reflected in work NRW has committed to do with respect to further investigations.
“NFU Cymru seeks assurances from Welsh government and NRW that the issues raised within the Panorama programme will be fully investigated."
The union is presently in the process of launching a legal challenge against Welsh government’s new rules to control agricultural pollution, having previously raised concerns about the lawfulness of the decision.