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This comes as the group awaits final approvals from the Spanish authorities so that it can start the redevelopment of theRio Tinto copper mine.
According to EMED, the board remains confident in the project. It now plans to bring in an appropriate new CEO to lead the company through to production.
Having advanced as much as 40% in September, to as high as 8.65p, EMED shares dipped around 9% following today's announcement in London trade.
City broker SP Angel said the sudden departure is a surprise, though, moving to appoint a new CEO with recent mining experience suggests the project is likely to go ahead.
"We are surprised to hear of the departure of Harry as the long suffering CEO of EMED Mining which has been through a protracted process of permitting to restart the Rio Tinto mine," said analyst John Meyer.
"He has had incredible staying power and has secured funding support for this project with all the hurdles put in front of him from landowners with vested interest and an impossible to fathom local and regional government structure for permitting in Spain.
"It looks now as if the project has a strong amber light to get government approval and looks likely to go ahead. Rod Halliday has been very involved in the project and is likely to take it forward with the support of a Spanish chairman."
"As the company moves into a phase of development and production, I have taken the decision to step down to allow the appointment of a new CEO with a skill set more appropriate to the future role.
"I would like to thank shareholders for their continued support and look forward to the company's transition into a major low cost European copper producer.
"EMED Mining is well placed as it approaches the production stage and I have full confidence in the ongoing team to take the project forward. It has been a privilege to have worked with EMED and the entire company's team, and to have the project advanced to its current state."
Chairman Ronnie Beevor said: "We would like to thank Harry for bringing EMED to this point in its journey to producer.
"We wish him well in his endeavours with KEFI Minerals and look forward to EMED's continued progress and success"
In the interim, as EMED looks for a new CEO, Rod Halliday will step up from his role as chief executive of subsidiary EMED Tartessus.
Disclosure: I have no positions in any stocks mentioned, and no plans to initiate any positions within the next 72 hours.