Charles said millions of small farmers around the world could be driven off their land into "degraded and dysfunctional conurbations of unmentionable awfulness" by the rise of global conglomerates.
The heir to the throne is a long-term supporter of sustainability and locally produced food and often speaks out on environmental issues.
He has an organic farm on his Highgrove estate in Gloucestershire and set up the Duchy Originals brand, which sells exclusively organic produce, in 1990.
But his latest comments have drawn criticism that he is a "Luddite".
The Daily Telegraph journalist who conducted the interview wrote that Charles "let rip" and started "jabbing his finger" and "bouncing in his chair" when asked whether large-scale food production was the future.
"What, all run by gigantic corporations? Is that really the answer? I think not. That would be the absolute destruction of everything and... the classic way of ensuring that there is no food in the future," Charles told the paper.
He added that "clever" genetic engineers had put the world on course for the "biggest disaster environmentally of all time."
The world should be working "with nature. We have gone working against nature for too long," Charles said.
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Labour lawmaker Des Turner, who is on the House of Commons science and technology select committee, criticised the comments, telling London's Evening Standard paper that Charles "has got a way of getting things absolutely wrong.
"It's an entirely Luddite attitude to simply reject them (GM crops) out of hand," he added.
Another Labour lawmaker, Ian Gibson, told the paper: "Prince Charles should stick to his royal role rather than spout(ing) off about something which he has clearly got wrong."
But the future king attracted support from environmental groups including Friends of the Earth.
"Prince Charles has hit the nail on the head about the damaging false solution that GM crops present," said its campaign director Mike Childs.
"GM crops will not solve the food crisis -- and forging ahead with an industrialised farming system will continue to fail people and the environment around the world."
The comments come amid rising concerns worldwide over rapidly rising food prices.
The World Bank estimates that food prices have almost doubled over the past three years, and its president Robert Zoellick has said two billion people are affected by the food crisis.
© 2008 Agence France Presse