The model, which is now in the hands of the UK advertising watchdog Ofcom, is designed to categorise foods on the basis of their nutrient content.
It aims to help rebalance children's diets by supporting Ofcom strategy of reducing the amount of advertising directed at children for foods high in saturated fat, sugar or salt.
But the Food and Drink Federation (FDF) argues that such a profiling system is unworkable as it is driven not by scientific concern but political agenda.
"The changes announced today clearly illustrate this," said FDF deputy director general Martin Paterson.
"The FSA announcement confirms that the final version of the model does not allow any foods which exceed a set threshold for saturated fat, energy, sodium or sugar to score points for the protein they contain unless they meet other artificial criteria."
The development of a nutritional profiling model has nonetheless been inevitable. Its creation was set out in both the government's White Paper entitled Choosing Health and the FSA's Action Plan on Food Promotions and Children's Diets.
And Deirdre Hutton, chair of the FSA, believes that the profiling model can provide the basis on which Ofcom can target action to cut down on unhealthy advertising aimed at kids.
"This technical model, which has been overseen by scientific experts, provides a systematic basis for categorising food," she said. "We know that children's diets are too high in saturated fat, sugar and salt and we want to redress the current imbalance of food advertising to children.
"We are confident that this model provides a sound and robust basis for Ofcom to use in its work."
The technical nutrient profiling model has been through three phases of detailed development during the past year. Final refinements were made in October to take into account feedback received in the second public consultation.
These include the belief that nuts should be scored in the same way as fruit and vegetables and that foods exceeding a threshold for saturated fat, energy, sodium or sugar should not be allowed to score for protein unless they contain high levels of fruit, vegetables and/or nuts.
The FDF remains unimpressed.
"We will be studying the model urgently," said Paterson. "We do not know what the detailed effects of the latest changes will be and neither, we believe, do the board of the FSA.
"FDF has today written to FSA Chair Deirdre Hutton to ask for clarification on this."
Ofcom will now consider how the model could be applied in its consultation looking at restrictions on broadcast advertising. The consultation is expected to be published in early 2006.