The scientists, who submitted their findings to the UK's Food Standards Agency (FSA) this week on behalf of pressure group the Independent Science Panel, believe that there are health and safety risks that have not as yet been taken into account.
Unilever on the other hand believes that the GM ice-structuring protein, derived from a polar fish, is completely safe and represents a major breakthrough for food makers looking to produce smoother and creamier ice cream.
The company said in its application to the FSA last month that it had used genetically modified baker's yeast, containing an ice structuring protein originally isolated from the blood of the fish, known as ocean pout.
Both the protein and the yeast is removed from the formula during processing, however, meaning nothing is passed on into the end product. Ice cream in shops would simply have ice-structuring protein on the ingredients label.
The transgenic protein is already used in ice cream in the USA, Australia and New Zealand.
But anti-GM campaigners such as the Independent Science Panel remain unconvinced. The group of scientists assert that, contrary to the claims of Unilever, there is no evidence that the transgenic ice-structuring protein is identical to the protein produced in pouter fish.
"The transgenic protein appears to have the glycosylation pattern of yeast, making that protein a unique antigen," said Joe Cummins, Mae-Wan Ho and Malcolm Hooper in a press release.
"Even though allergenicity was studied in a cursory way, there is clear precedent for studying inflammation comprehensively in the long term in both young and older animals before exposing the European public to the transgenic ice cream."
Whatever the success of the Independent Science Panel's intervention, the issue highlights yet again the huge fault line that runs through any European debate over the safety of GM; though increasingly, food safety is no longer the main arena for conflict.
A major catalyst for this paradigm shift was the landmark WTO decision in February, which ruled that the EU and six member states broke trade rules by barring entry to GM crops and foods. By agreeing with the United States, Argentina and Canada that an effective moratorium on GM imports between June 1999 and August 2003 had been put in place, the ruling effectively opened up the European market to GM food.
In any case, the move makes Unilever the latest in a number of major food firms to announce its intention to penetrate further into the low-fat ice cream market. Indeed, the firm is likely to face increasing competition in the healthy ice cream market, with several other firms unveiling new techniques for low-fat ice cream in recent months.
For example, Dutch firm Unimills recently claimed to have developed a way of slashing saturated fat from butter-based ice cream. This came only days after US-based firm FMC Biopolymer announced it had devised a new, cellulose-based ingredient to cut fat in ice cream down to five per cent.
And European ingredients giant Danisco has also said that it can make ice cream with less than one per cent fat, thanks to a new ingredient blend based on its Cremodan IcePro technology.
Unilever expects to find out this month whether its protein ingredient has been approved in the UK.