The European office in Belfast confirmed that the project - part of a Pounds 250 million package of aid for the province and the border counties of the Irish republic - was unique within the terms of the commission's work.
The package aims to "change social attitudes so that the traditional hostility to the 'other' community is diminished and challenge the mono-cultural development of children".
Jane Morrice, head of the EC office in the province, said it was the first time specific mention had been made of this type of action in any programme run by the European Union.
And she said: "I personally believe that the only way we can begin to eradicate suspicion, fear, hatred, bigotry and discrimination in this region is by starting at the beginning. That means getting young kids together - Catholics and Protestants - from the very earliest age."
But the move will cause a furore with the other segregated sectors in the province who already complain that the integrated schools have an unfair advantage.
David Allen, chairman of the Teachers' Council, which represents all the main teacher unions in Northern Ireland, said the EC backing was ill-advised and would create disharmony and lead to redundancies in the mainstream sector.
"If the Commission wants to help it should fund a very essential part of education where children have been integrated for years - the nursery schools, which would have a long-term impact on reconciliation and peace," he said The unexpected financial boost comes after the integrated movement has won a victory over the Department of Education which wanted to transfer funding for mixed schools to the area boards (local education authorities). The NI Council for Integrated Education complained the change would destroy an effective relationship and threaten the independence of the growing number of integrated schools.
Activists fear the peace process could mean integrated schools would be given a lower priority in future policy. Also, the possibility of a future new elected assembly with more local control of education could consolidate the existing divided structure of controlled (mainly Protestant) and maintained (mainly Catholic) schools.