East Riding of Yorkshire Council refused planning permission for the River Valley Wind Farm in July 2013 against an officer recommendation for approval.
Developer RWE Innogy then appealed against the decision.
The proposal was for six 128 metre-high turbines on agricultural land next to Welham Bridge near Spaldington.
The appeal was recovered for the secretary of state’s determination in December.
Pickles has now backed the recommendation of planning inspector, John Woolcock, who concluded that the appeal be dismissed, citing concerns over impact on the landscape and potential harm to heritage assets in the area.
The decision letter explained that the secretary of state agreed with the inspector’s planning balance, agreeing that the development could make a "significant contribution" to renewable energy targets, but "the cumulative effects of the appeal proposal along with existing and consented turbines are particularly important in this case with respect to the likely impact on the character and appearance of the area and on heritage assets".
He concluded that "the identified harms are not outweighed by the scheme’s benefits, that the scheme is not in overall compliance with the development plan and that it does not amount to sustainable development".