Amazon said that James's erotic novel Fifty Shades of Grey is also the number one best-selling Kindle book of all time at Amazon.co.uk.
James, who originally self-published her books online and on Kindle Direct Publishing (KDP), has generated more than one million Kindle sales for the Fifty Shades trilogy, despite the first book only being released a year ago.
The Kindle version of Fifty Shades of Grey is said to be currently outselling the print book in the UK at a rate of more than two to one.
"E L James's books have become both the fastest-selling and the best-selling series ever on Kindle," said Gordon Willoughby, the director of EU Kindle.
"That's an exceptional achievement for a debut novelist and we're excited to see her pass the one million sales milestone.
"Following a stint of self-publishing, first online and then via KDP, E L James found a fanbase and her success has rocketed from there.
"Her books have become a worldwide phenomenon demonstrating what a powerful launch pad KDP can be."
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Alongside the digital success on Kindle, Fifty Shades of Grey, Fifty Shades Darker and Fifty Shades Freed are currently the number one, two and three best-selling print books at Amazon.co.uk.
Their combined sales have made James the best-selling print author so far in the UK in 2012.