An inspector appointed by the Secretary of State for Environment, Food and Rural Affairs dismissed the appeal at Catfield, Norfolk, following a public inquiry. The licences were used for crop irrigation.
NFU national water resources specialist Paul Hammett said: “This is disappointing news for local farmers and for irrigated crop production in the immediate vicinity around Catfield Fen.
“The NFU now needs time to consider the inspector’s report in full before responding in detail.
“It’s important to remember that many of the issues raised during the public inquiry were site-specific. This means that wider implications of this decision are likely to be extremely limited.
“Much of debate at the inquiry centred on the Habitats Directive. Our members have significant concerns about the adverse impact the Directive can have on farming and food production activities in the vicinity of a protected site.
“Under the current precautionary principle farmers have to prove they are not causing harm, rather than harm be evidenced. Proving a negative is always extremely difficult to do.
“However, this case was never about changing the Habitats Directive, the principles of which are well established in EU law, but about how its rules are applied at one specific location.”