Multinational aggregates company Lafarge has applied to build the quarry on Harris, but the Scottish Executive rejected the proposals, saying that the benefits would not outweigh the environmental impact. Lafarge is appealing against the decision in the High Court in Edinburgh this week.
Lafarge is a founding member of the WWF Conservation Partner programme and has donated the £3.5m to WWF International, which shares the money among its national member organisations.
Simon Pepper, director of WWF Scotland which speaks on this issue for WWF UK, said: "WWF International and Lafarge both operate on a global basis. We believe that partnership is delivering achievements on a number of environmental issues, such as reducing carbon dioxide emissions. But for Lafarge to return to this issue after the superquarry had been rejected by a minister and a public inquiry was going too far."
The decision to return the money to WWF International was taken by WWF UK's chief executive, Robert Napier. Before working for the WWF, Napier was chief executive of Redland, the company which first applied for permission to open a quarry on the island of Harris, and which was subsequently bought out by Lafarge.
Two instalments were returned in February and June. Another instalment, due now, will be refused. "The money from Lafarge is distributed to all parts of the network, and our share doesn't amount to more than a few thousand pounds," said Pepper. "The issue is that WWF UK was publicly opposed to the quarry on Harris long before the partnership, and we rejected the money because we didn't want to create confusion about our position."
Friends of the Earth Scotland chief executive Duncan McLaren said: "Some may see this as biting the hand that feeds. But we see this as a genuinely ethical action - something Lafarge itself has so far seemed incapable of."