But Mr Congdon was accused of hypocrisy over the arrangements, which appeared to fly in the face of Ukip’s anti-wind farm stance.
The party claims the developments are economically “unsustainable” and eyesores that blight the countryside.
Last night it emerged that Mr Congdon had stood down as economics spokesman following the row. But it is thought he wants to remain as the party’s candidate in the Forest of Dean where he is due to stand in the 2015 General Election.
His resignation will place further pressure on Ukip.
The party has come under scrutiny in recent months, as the party gears up for the European Parliament elections.
Ukip is expected to do well in the UK-wide poll, potentially even beating the Conservatives.
Last month Mr Congdon admitted his actions regarding wind farms had been “maybe hypocritical”.
He struck a deal with SSE to allow them access to a track through three forests that he owns in Kintyre in order to build a 10-turbine wind farm at Cour.
When asked he refused to disclose how much he receieved.
In 2010, Mr Congdon signed another agreement, this time with E.On Climate & Renewables UK Developments Ltd, for a wind farm at his Hollandmey Forest in Caithness.
He was entitled to early test and lease payments, although E.On chose not to proceed with the site in the end.
The terms included a £10,000 “option fee” and £25,000 “Hollandmey Farmhouse Compensation”.
A Ukip spokesman said: “Professor Congdon stepped down over a week ago, and we agreed to his resignation. Discussions are still going on about what to do in the Forest of Dean.”