Gregory takes charge of the research station in Kent from 1 May 2011 while also taking on the role of professor of global food security at the University of Reading.
Until recently Gregory was the chief executive of the Scottish Crop Research Institute (SCRI) where he built strong research collaborations between SCRI and its partners. In his new roles Gregory will spend four days a week at EMR and the remaining day at the University of Reading working with the new Centre for Food Security and its director, Professor Richard Tiffin.
Gregory said: "I am delighted to be joining EMR as chief executive at a time when fruit and food are back in the public eye.
"My role at Reading will allow me to project EMR's work internationally and to bring a new generation of students into direct contact with the practicalities and challenges of producing and marketing high-quality horticultural foods."
EMR chairman Dr Oliver Doubleday said: "I am confident Peter is just the person to guide EMR's development as one of the UK's main horticulture research and development providers and extend its remit."
Gregory spent most of his career at the University of Reading but has also worked overseas on projects seeking to increase crop production.
Peter Gregory's appointments are expected to further strengthen the tie between EMR and the University of Reading after they signed a Memorandum of Understanding last year to foster academic, scientific and cultural collaboration.
The institutions are already collaborating on aspects of the National Fruit Collections at Brogdale, which is managed by the University of Reading on behalf of Defra. It is hoped that more co-operation will benefit national and international food and health security.