Sir David King said concerns which had greeted the technology had proved "unreal".
GM products were probably safer for consumers than food produced in the conventional way, he said.
And he added that, with its pioneering role in molecular biology, Britain was well-placed to develop a safe technology which would be vital for feeding the world's population.
Sir David steps down as chief scientific adviser at the end of 2007 after seven years.
Last night, he used a valedictory speech at the Royal Society to argue the case for GM food.
He said: "By mid-century, the population will have reached 9.5 billion. We have got a planet with overstretched resources. If we are going to feed that population we need the technology that can deliver that, and we have the technology. It is GM."
He acknowledged that a large proportion of the population had worries about the development of GM products.
But he said: "There are all sorts of concerns that are turning out to be unreal."
Sir David said tight regulation was necessary to ensure that GM was developed in a way which allayed public anxieties, and said Britain had shown itself able to put the right regulatory framework in place.
"It is a highly sophisticated technology," he said. "We have to introduce stringent regulatory procedures so we can treat the products case by case.
"Quite clearly, we have to have regulation to see that we protect our biodiversity, to see we protect our crops and to see that we feed the population. We have to get all these things together."
He added: "Because the technique is so sophisticated, in many ways it is probably safer for you to eat genetically modified products - plants that have been generated through GM - than normal plant foods, if you have any sort of reaction to food, because you can snip out the proteins that cause the negative reaction to certain parts of the population."
He said: "Britain is the country that invented molecular biology. We have the technology to develop GM plant foods sensitively so that we deal with the challenges of the future."
The Prime Minister, Gordon Brown, responded by saying he did not share Sir David's opinion. "We are not in that position at the moment. It seems to me there is only one approved GM crop in Europe," he told reporters at a Downing Street press conference.
He added that he would have to look at commercial proposals brought forward.