The NFU is calling for an investigation to ensure agriculture has not been impacted or blamed for illegal sewage discharges following the issue being raised by BBC Panorama.
'River Pollution Scandal' - aired on 12 April - appeared to show untreated sewage being illegally discharged into protected rivers in England and Wales.
The BBC programme analysed data that showed some water companies had regularly breached the conditions in their permits.
Investigators also found an incidence where a water company failed to report multiple discharges of untreated sewerage to the Environment Agency.
An NFU spokesperson said the issues raised in the Panorama programme were 'very concerning'.
The union said it had already raised concerns about misattributed pollution to Environment Agency as recently as 2019.
"We would like to be assured that full investigations are undertaken to ensure that agriculture has not been unfairly disadvantaged by, or been held accountable for, any alleged illegal discharges from sewage treatment works.
“What we do know is that Britain’s farmers are taking their environmental responsibilities incredibly seriously," the spokesperson added.
"Significant strides have been made, with the number of serious agricultural pollution incidents nearly halved year-on-year and reduced by over 75% compared to 2000.”
NFU Deputy President Stuart Roberts wrote to the Environment Agency in 2019 to seek assurances on self-reporting by water companies.
It follows an investigation by the UK's water regulator which found Southern Water deliberately misreported its performance at a number of sewage treatment sites.
Although the NFU did receive such assurances at the time, the union said the new allegations made in Panorama raised 'fresh questions' for water firms and the EA to answer.