Professor Patrick Bateson, vice president of the Royal Society, told the BBC that he saw "no evidence" that genetically modified crops were causing environmental damage.
But campaigner Dr Sue Mayer argued there was a "conflict" between organic farmers and GM crop testing.
They were responding to the Prince's calls for GM research companies to be made liable for harming the environment.
'No good evidence'
Prince Charles said the emphasis seemed to be on backing GM crop research which "posed an acute threat to organic farmers" regardless of a possible environmental threat.
He said consumers were being denied choice by governments supporting GM crops over increasingly popular organic food - despite consumption growth of 15% a year.
But Professor Bateson, of the UK's national academy of science, told BBC Radio 4's Today programme: "As far as I can tell, I have lost choice over what I can buy in the supermarket as a result of the hysteria over GM foods."
And he said he had seen "no good evidence" that GM crops have a detrimental effect on the environment.
"On the contrary it seems to have led to an improvement in environmental conditions," he said.
Wider concerns
Dr Sue Mayer, executive director of Genewatch, said organic farmers were under threat because of GM crop growing.
And she argued that the issue would become "much more acute" for farmers in the future.
And she said the organic industry needed safeguarding.
"It is very urgent that we protect the interests of a really growing organic farming industry - which is healthy for the environment," she said.
Prince Charles spoke in the German city of Lubeck after accepting the 2002 Euronatur Award for his efforts to protect the environment.
The Prince talked of the threat of GM research to organic farming, depleting fish stocks in the North Sea and the use of plastic corks in wine bottles.