It made the claim at an appeal hearing into the case of Peter Boggis, who last year won a High Court case ruling that Natural England had acted unlawfully by allowing part of the Suffolk coast to erode. Mr Justice Blair backed Boggis's argument that his "human predicament" must take precedence.
Natural England wants fossil-bearing cliffs near Southwold to be allowed to erode naturally for scientific reasons. It disputes the ruling that its plan is unlawful because it failed to carry out an assessment of how a nearby wildlife haven might be affected.
Since 2002, Boggis has spent tens of thousands of pounds installing sea defences near his Easton Bavents home. John Howell QC, acting for Natural England, told Lord Justices Mummery, Longmore and Sullivan that these were built without permission or an environmental impact assessment.
The area has been a site of special scientific interest since 1982 and Natural England wants to extend the designation to Boggis's land. The Court of Appeal judges are due to give their ruling at a later date.