An interim CEO will join EDC in January. It has been reported that the Department of Communities and Local Government wanted a CEO with fewer close ties in the county.
EDC chairman Michael Cassidy said Cooper had been involved in the setting up of the corporation through its early phase of development.
"We now move into a focused delivery phase where recruitment of experienced project managers will be a priority. The interim CEO will be well-placed to oversee this part of the programme. We wish to express our thanks for Robin's considerable efforts in helping us to date."
EDC secured £310m of Government investment in November's Comprehensive Spending Review, to fund the building of 15,000 homes. The Government is billing Ebbsfleet as the first garden city in more than 100 years.