Dr Bill Parish, a senior ecologist in the Department of the Environment, was the scientific brain behind the GM farm scale trials and was in charge of administering them.
The ecologist wrote the seminal research paper that changed the course of thinking about the effects of growing GM crops on the environment and was the man who first alerted the Government to their potential effects on wildlife. He was also one of the small group of experts assessing whether GM crops should be grown commercially in the UK.
Dr Parish is one of only a handful of civil servants ever to be named by ministers as a research author and his decision to leave has shocked the Government.
The scientist is regarded as "a right-hand man" to ministers and has helped shape GM policy in the European Union.
"He has an absolutely crucial job in directing policy on the GM trials and is relied on for his advice," said one government source. "He is one of the few experts we have in his field. This is a big blow to us to lose him."
Dr Parish, who has left to "pursue research", was head of the ecology branch of the Department of the Environment's biotechnology safety unit. Civil servants in the unit, which shapes policy on GM crops, have come under severe pressure in recent months because of the controversy surrounding the GM trials.
The civil servants have had to deal with the demands of biotechnology companies, which have been trying to persuade government to allow them to go ahead with commercial planting.
They have also have been responsible for liaising with farmers whose experimental crops have been destroyed or damaged by protesters who fear that they are harming the environment.
Most supermarkets have now declared their own-brand products GM-free because of pressure from consumers.
The Government recently set up a special spin-doctoring unit in the Cabinet Office to try to deflect criticism from GM foods.