Claims by former minister Michael Meacher that the UK Government played down a report criticising the safety of GM food have been denied by an environment spokesman.
An official at the Department for Environment, Food and Rural Affairs (Defra) said the government regarded both health and environment as "top priorities".
Trials of GM crops are due to finish later this year
Mr Meacher has revealed he was sacked as environment minister - a post he had held since the 1997 election.
It had been suggested that the veteran of the Wilson and Callaghan administrations had quit the government.
His views on GM foods are believed to have been increasingly at odds with those of the prime minister.
In an article for the Independent on Sunday, Mr Meacher accused the government of deliberately undervaluing negative research findings on the safety of GM foods.
He said scientific reports indicating possibly damaging effects on humans had been "widely rubbished in government circles".
And the debate on GM foods had been deliberately stifled with pressure from bio-technology companies, he said.
But a spokesman for Defra said: "Both GM crops and foods have to undergo rigorous safety assessments before they can get approvals.
"These approvals require there is no risk to health or the environment."
He said a public debate on the GM issue was under way, and people were welcome to contribute views.
GM crops have attracted widespread opposition
Liberal Democrat environment spokesman Andrew George said Mr Meacher's comments "blow a hole in any claims the government might make about their desire for an open debate on GM".
Anti-GM campaigners welcomed Mr Meacher's comments on Sunday.
Pete Riley, of Friends of the Earth, said they confirmed the fears of those who suspected the government-funded debate on the GM issue was a mere PR exercise aimed at getting the green light for GM crops to be grown in the UK.
Patrick Holden, the director of the Soil Association, which campaigns for organic food and farming, said: "Mr Meacher's comments are very worrying because they suggest the government has already made up its mind on GM."
But a farmer involved in GM crop trials claimed some of Mr Meacher's comments were "inaccurate".
Bob Fiddaman, who is also a board member of pro-GM group Scimac (Supply Chain Initiative on Modified Agricultural Crops), said: "The GM foods that are released for human consumption have been tested and there are no known negative effects on humans."
Mr Meacher said studies on the effects of GM foods on human health had been "scientifically vacuous", and warned the government against rushing the debate.
Adequate testing, sound scientific conclusions and an understanding of the effects on people were still lacking, he said.
"Since the science is still clouded with such deep uncertainty, that means deferring decisions till the science is clear and reliable, not rushing to desired conclusions which cannot be scientifically supported," he said.
He told the Independent on Sunday the only human GM trial commissioned by the Food Standards Agency found genetically modified DNA did transfer to bacteria in the human gut.
Many scientists had denied this was possible.
"But instead of this finding being regarded as a serious discovery which should be checked and rechecked, the spin was this was nothing new and did not involve any health risk," he said.
Some GM substances had already been found to cause allergic reactions, he said.
Mr Meacher is unconvinced by GM crop tests
There were concerns the development of pesticide-resistant GM crops meant consumers were being exposed to increasingly toxic residues, some of which could damage embryos in the womb.
Mr Meacher said the so-called rigorous testing of GM products only amounted to considering whether a crop was similar in composition to a non-GM crop.
"This is justified under the rubric of 'substantial equivalence', which was originally a marketing term, and is scientifically vacuous".
He said it was "really extraordinary" there had so far been virtually no independent studies of the health effects of GM.
Mr Meacher has pledged to continue campaigning on environmental issues from the back benches.
The government launched a series of nationwide public consultations on GM crops earlier this month.