The charity published a report about the tech giant's practices titled 'How Clean is My Cloud?' in which it was alleged that Apple powers its data centers using 55% coal energy.
Greenpeace singled out the company's plants in Maiden North Carolina and Prineville Oregon for criticism, claiming that both are reliant on "dirty power" such as coal and nuclear.
Activists from the charity targeted Apple's Regent Street store in London this week, plastered the windows of the branch with leaflets about energy consumption, and spoke to customers and staff about its perceived implications.
Apple has since contacted Digital Spy to reject the findings of Greenpeace's study, claiming that the thrust of the allegations is based on factually incorrect information.
The firm added in a statement: "Our data centre in North Carolina will draw about 20 megawatts at full capacity, and we are on track to supply more than 60% of that power on-site from renewable sources including a solar farm and fuel cell installation which will each be the largest of their kind in the country.
"We believe this industry-leading project will make Maiden the greenest data centre ever built, and it will be joined next year by our new facility in Oregon running on 100% renewable energy."
Apple also claimed that the charity's report did not use an accurate number for Duke Energy's coal mix in the area. "The DukeEnergy grid mix for 2011 shows coal at 45% and not the 61% reported," the firm added.
Meanwhile, Apple confirmed this week that its Worldwide Developers Conference (WWDC) will get underway in June, with new announcements expected on iOS and OS X, but not the next-generation iPhone.