In an interview with The Grocer magazine, she said those who were opposed to all GM foods were guilty of a "huge simplification" and that organic food production is not an "overall answer".
The Princess, who is the President of the British Association for the Advancement of Science, told the magazine: "Man has been tinkering with food production and plant development for such a long time that it's a bit cheeky to suddenly get nervous about doing it when fundamentally you are doing much the same thing.
"Of course shoppers feel the speed of change is too fast to understand what the dangers are and where the weak points might be. And that seems to me to be a perfectly valid argument.
'Life's not simple'
"But it is a huge oversimplification to say all farming ought to be organic or there should be no GM foods. I'm sorry - but life isn't that simple.
"You can add value on the marginal farms through organics. But I feel they're not an overall answer.
"If you consider things in terms of overall production and sheer weight of numbers, of supporting a population which has so hugely increased, then organics is not the whole answer," said Princess Anne.
Her brother is a long-standing advocate of organic farming techniques and, in a Reith lecture broadcast on BBC Radio 4 last month, said that "nature has come to be regarded as a system that can be engineered for our own convenience ... and in which anything that happens can be fixed by technology and human ingenuity".
He added: "If literally nothing is held sacred any more - because it is considered synonymous with superstition or in some other way irrational - what is there to prevent us treating our entire world as some great laboratory of life, with potentially disastrous long-term consequences?"
He welcomed a "precautionary approach" to scientific advances and mocked those who portray it as a sign of weakness or an attempt to halt progress, saying: "I believe it to be a sign of strength and wisdom."
He said: "In this technology-driven age, it is all too easy for us to forget that mankind is part of nature and not apart from it, and that this is why we should seek to work with the grain of nature in everything we do."