Sir David King has attracted controversy in the past for his pro-GM stance in the past and - most recently - for advocating a cull on badgers to curb tuberculosis.
He will give up the post he has held since 2000 at the end of this year, and this week gave a valedictory speech at the Royal Society in London.
In the speech, Sir David reportedly said he believes many of the concerns about GM foods have proved "unreal".
Moreover, he proposed that GM as a solution to ensuring sufficient food supply for the world's growing population in the future, which is expected to be problematic this century.
In an interview with the BBC prior to the speech, he said we will need a "third green revolution" to feed the world's population of 9.5 bn by mid-century.
"Have we got the technology to deliver that?
Absolutely.
It's called GM technology."
Friends of the Earth, however, takes issue with the claim that GM foods are safe.
In its opinion, genetic engineering is "imprecise and unpredictable".
It claims most of the testing is carried out by the biotech companies that have developed GM in the first place - and therefore have much to gain financially from declaring them safe.
It also denies there is a need for GM in the world.
The UK has, historically, been one of the EU member states that is more supportive of GM technology - or at least, not vehemently anti.
Indeed, Sir David led a GM science review, which concluded its work in 2004, that found "no scientific case for ruling out all GM crops and their products, but nor does it give them blanket approval."
It said that GM applications need to be considered on a case-by-case basis, but that GM regulation needs to keep pace with new developments.
Some of the UK's neighbours and other notable member states have taken a rather hardline anti-GM approach.
French president Nicolas Sarkozy recently announced a moriatum on the planting of commercial GM crops, pending a four-month consultation to establish a policy on GM and the environment.
And the Austrian government has been grappling with the EU over its ban on cultivation of two types of GM maize for several years.
The deadline for the Commission to reach a consensus on how to deal with states implementing their own bans was recently extended by the World Trade Organisation to 11 January 2008, after ministers failed to come to an agreement.
In June of this year, EU trade commissioner Peter Mandelson delivered a strong exhortation to the EU to take a lead in shaping global rules on GM trade - particularly in defending objective science as a benchmark - or suffer the economic consequences.
He called biotechnology "the coal face of applied science in the 21 st century", and said that if the EU does not work through the issues raised by genetically modified (GM) food, just as the rest of the global market is doing, it will not be working it its own best interests, he said.
And if the EU falls behind in approving safe biotechnology, it would open itself up to economic risks.
Sir David's opinion has been that the UK's strong position in molecular biology research means it is well positioned to develop GM technology safety.
Away from Brussels and Westminster, however, there are indications British consumers remain wary of GM foods.
The British Retail Consortium has indicated that resistance remains strong - and unless the majority of shoppers swings to support GM then the foods are not going to be making a splash on shelves.
The Soil Association recently conducted a survey of the use of GM feed for animals used to produce milk and dairy for human consumption in the UK.
It said it was " shocked to find that very large quantities of GM feed are being used in the UK to produce our food".
It said that around 60 per cent of the maize and 30 per cent of the soya in the feed used by dairy and pig farmers is GM.
"This means that most of the non-organic milk, dairy products and pork being sold in the UK is from GM-fed animals," said the association - but it does not need to be labelled as such.
Moreover, it said there is evidence to suggest that small amounts of GM DNA make it not the milk and tissues of GM-fed animals.
This opinion is contrary to those held by the Food Standards Agency and the British Retail Consortium.