Field trials were conducted on land owned by the University of Milan to determine the benefits of GM crops and the possible dangers they pose to consumers.
The outcome showed that, as well as resisting the corn borer pest without the use of pesticides, the P67 and Elgina maize varieties helped reduce the content fumonisin toxins, say the scientists.
But the results of the trials were never formally published, spurring scientists to accuse the government of suppressing the information because of its anti-GMO stance.
Meanwhile, the state-run National Institute for Research of Food and Nutrition (INRAN) today issued a statement saying it had not actually received the results as claimed.
INRAN added that it has actually conducted its own analysis, which goes further than the original results, and that it now deems suitable for publication.
Fury over fumonisins Fumonisins are toxins produced by fungi that can infect a growing maize plant.
There is evidence to suggest they increase the risk of spina bifida in humans, and can cause other illnesses in horses and pigs.
Roberto Defez, group leader in microbial biotechnology at the Institute of Genetics and Biophyscis, explained that Italy has serious problems with fumonisins.
"The problem is officially known," he said.
"Over forty per cent of the maize produced contains more than the maximum levels of fumonisin."
The information on the study only came to light when Tommaso Maggiore, the agronomist who conducted the trial, realised the results would not be published and approached the scientific community through Defez, and scientists at the University of Milan, to get the information into the public domain.
Defez told FoodNavigator.com that, as it stands, the results from the study are not a major contribution to scientific research.
He said: "What we are asking for is that the ban be lifted so the trial can be repeated by the scientific community, to compare and evaluate to see whether this is a usual result, and can therefore benefit Italian agriculture."
Legal issues in Italy Defez explained this was the first trial on genetic modification in Italy for seven years as such studies are illegal in Italy.
Funded by the ministry of agriculture under an investment of €6.2m, it did not come under the ban as the maize is allowed for consumption in Europe, therefore not described as experimental, and it was not planned for commercial cultivation.
When the results were allegedly handed to the INRAN early last year, they were never formally published in a peer-reviewed scientific journal.
In addition to denying it had received any results, INRAN said it had not asked Maggiore to perform the fumonisin analysis.
Study results The fumonisin-producing fungi infect a maize plant by entering through a wound, which can be inflicted by the European corn borer.
At the trials, no corn borer larvae were found on the Bt varieties, while an average of 29 of the pest were found on each stalk of the conventional varieties.
In INRAN's statement today, it said that its analysis actually found 81 per cent higher levels of the fumonisin in the maize that was not genetically engineered.
According to Maggiore's results, using the GM maize also increased the volume of grain produced, yielding between 14.1 and 15.9 tonnes per hectare compared to between 11 and 11.2 tonnes of grain per hectare.
This relates to a yield increase of between 28 and 43 per cent, translating into a difference in profit of between €300m and €1bn.
Opposition to government policies The issue has now been documented in the Italian media, and opposition parties have spoken out against the government's anti-GM stance.
Radical MP Marco Cappato accused the government of "prohibitionism and violation of the freedom of research", while Tortoli from Forza Italia called for an increase in research.
Belloti, from the Alleanza Nazionale, said: "The demonisation of GMOs is the result of an ecological ideology that smells of hypocrisy."
Issues surrounding GMOs Despite the beneficial effects on plant disease of GM maize found in this single study, concerns have been raised over its health risks to humans.
In March, it was revealed that the Monsanto maize MON863, authorised for human consumption since 2006, showed signs of liver and kidney toxicity in a rat study performed by French researchers.
However, after reviewing the data, the European Food Safety Authority rejected the concerns in June this year.
Genetic engineering goes against the increasing consumer trend for natural and organic products as fears have arisen over a lack of knowledge of its long-term effects.
Environmental campaigners have also highlighted the impact on non-target species and there have been worries over the risk of contaminating non-GM crops.