The report conceded that Defra needed to implement the Directive to halt EU legal proceedings currently being taken against the UK, but described the proposals as impractical.
Efra committee chairman Michael Jack MP said Defra's proposals for implementing the Nitrate Vulnerable Zones (NVZs) would place "considerable financial burden on livestock and dairy farmers at a time when they are ill-equipped to meet these costs".
NFU president Peter Kendall said: "From its report the committee recognises the flawed and dated nature of the Nitrates Directive and that Defra's original proposals will place massive costs on farmers across England.
"However, we acknowledge Defra must act and we join the committee in calling for fair and well-reasoned measures.
"NVZs are a massive priority for the NFU, just as the Efra Select Committee recognises. I am proud of the effort we have put into our NVZ lobbying: meeting MPs, hosting farm visits and employing a consultant to test the nitrates database. Defra must justify the measures it proposes."
As the only group to provide oral evidence during the committee's enquiry, the NFU is calling for substantial changes to the NVZ programme.
"We are urging ministers to scrap plans for autumn cover crops, to match slurry storage for closed periods and to only designate NVZ areas where the science demonstrates a case", said Mr Kendall.
"We also need a reasonable time to install the new storage; Defra's proposal of two years is totally unrealistic. The Efra Select Committee's recommendation is far more pragmatic.
"The NFU is encouraged that the select committee also calls on Defra and the Treasury to provide financial support to implement these measures. With up to 5,000 new slurry stores needed and costs averaging £50,000 a farm, government must provide help to invest - just as other member states are doing across Europe."