The proposed four-turbine development in Highbridge, Somerset, known as the Black Ditch wind farm, would be located in the Somerset Levels and Moors national character area, designated by conservation adviser Natural England.
The inspector examining the case concluded that, while the turbines would have a significant impact on the immediate landscape, it would be able to absorb the turbines without significant harm, and that in long-range views the turbines would appear relatively small.
In a decision letter issued earlier this year, Pickles agreed with the inspector on these points. But he said that the scheme's landscape and visual impact "would be significantly adverse from viewpoints within about 2 kilometres of the appeal site".
Pickles said he did not think the harm the wind farm would cause to the landscape and its visual impact would be outweighed by its benefits.
A spokesman for Ecotricity said: "Following a review of the secretary of state's decision to dismiss our appeal for four wind turbines at West Huntspill, and in particular aspects of the decision-making process relating to landscape and topography at the site, we have decided to challenge the decision.
"We have conducted several years of environmental assessments at the site. The positive results of those assessments, as well as recommendations for approval from both the council's planning officer and the planning inspector, strongly suggest that Black Ditch is absolutely an appropriate location for four wind turbines."
This is not the first time Ecotricity has come up against the UK government. Last month, the company announced it was shunning the UK government's new subsidy regime in favour of the old one for a planned 54MW project in Lincolnshire.