Green set up a deal with Moss last month, in which the supermodel will design a range of clothes for the popular fashion chain.
It was reported yesterday that Shepherdson, who has been tagged as one of the most powerful people in fashion after turning around the fortunes of Topshop, was leaving after the deal was signed with Moss.
However, any rift has been denied by Green who says Shepherdson has resigned after deciding it was "time for a change".
In addition, Green went on to say that Shepherdson was fully behind the tie-up with Moss.
Shepherdson has been with Topshop for 18 years. She is renowned for transforming the business into a favourite for young shoppers and celebrities.
In December, Shepherdson came in at number seven, above Tony Blair, as one of London's top movers and shakers in a list compiled by Time Out.
Green is the billionaire owner of Arcadia retail group that includes Topshop.
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