The NFU has said it is "disappointed" after the Environment Agency rejected its recommendation to delay the implementation of changes to its charges regime until at least April 2019.
Earlier this year, the NFU called on the Environment Agency (EA) to delay changes to its charging regimes due to the significant increase of costs for farming businesses.
The farming union called proposed increases, unveiled in November, as "disproportionately high" which could have a "detrimental effect" on many farm businesses.
However, the EA has now rejected the NFU's recommendation for a delay in its implementation, and the new charging schemes for regulatory permits and services will be effective from 1 April 2018.
Changes affecting the farming sector include an increase in charges for land spreading, with the NFU criticising the move as "disincentive."
NFU environment forum chairman Mark Pope said farmers with groundwater authorisations for the land spreading of sheep dip, a land spreading of waste permit, anaerobic digestion for on-farm activities or are involved in permitted flood management activities will be "extremely concerned" that instead of investing in their businesses they will be hit with "inflated administrative costs".
Mr Pope explained: “We want farming to continue to improve its environmental performance, but these cost increases could be seen as a disincentive to improve management practices or limit the availability of management options in the future.
“What is important is that the NFU maintains discussions with the EA to continue to find ways of keeping the increased costs to a minimum.”
The EA has also confirmed a reduction in the annual variation charge for all existing intensive farming sites. Permit application fees for new intensive farming sites will rise.
NFU environment forum chairman Mark Pope said: “The cost for the 1,250 or so poultry producers who would have incurred a variation charge as a result of a review of technical standards will be reduced which is good news.
“This will now be £380 for those that complete preparatory work, instead of a previously proposed fee in the region of £2,406 - £7,218.”
The EA has also announced that there will be increases to application and subsistence charges for flood risk activities.
The NFU says the new charge scheme will better reflect the true costs of determining permits and monitoring compliance, and remove reliance on grant in aid funding.