This has been greeted with little surprise since it was not regarded as achievable.
In a significant change of tack, announced in a short pamphlet slipped out without ceremony via the Executive's website on Tuesday, the new expectation is that "by 2007, every school will participate in delivering integrated children's services".
The Executive believes that "it no longer makes sense to think of schools separately from other agencies". The wider integrated children's services agenda, in which all agencies such as schools, social work and health are required to collaborate, is said to have overtaken the initial policy.
Officials also point to the qualities schools are expected to nurture in pupils as set out in A Curriculum for Excellence - confident individuals, effective contributors to society, successful learners and responsible citizens.
All children therefore have to be "safe, nurtured, healthy, achieving, active, included, respected and responsible (and) this can only be achieved if all professionals working with children and young people pull together to plan and deliver top-quality services which overcome traditional boundaries", the pamphlet states.
A spokesman for the Executive said: "Our approach is that integrated working should not be seen as a separate part of a school's work but should be a fundamental part of what every school does and what every service involved with children does."
The pamphlet notes that several policies, notably the development of health-promoting schools, enterprise education and eco schools, will in any case require schools to work with other agencies. However, the ingredients that have been absent from integrated working are implicitly acknowledged.
The statement accepts that success will only happen "where there is strong leadership and commitment at all levels through local authorities, school senior management teams and in the classroom".
The HMIE report on integrated community schools, published in 2004, found there was a lack of commitment. "Too often, the approach adopted operated in isolation from mainstream activity without the right kind of leadership and vision at senior levels," Graham Donaldson, head of the inspectorate, said at the time.
Bert Biagini, the lead inspector for the report, commented: "There is still some way to go if the main aim of the original concept of the school - being the hub through which better integrated services for children and young people could be delivered through health, education and social work - was to be achieved."
The inevitable outcome has been welcomed. Bill McGregor, general secretary of the Headteachers' Association of Scotland, said he was "disappointed but not surprised".
"The principle of integrated working is very sound but we had severe doubts about the ability to deliver it, particularly on the part of the other partners in the exercise," Mr McGregor said. "It was often given a low priority."
Ronnie O'Connor, president of the Association of Directors of Education in Scotland and Glasgow's executive director of education, said: "What we need is better inter-agency collaboration at school and cluster levels, in a more collegiate approach involving all services for children and operating with greater consistency."
The approach now being taken by the Executive is essentially what his council's new learning communities are striving to achieve. Based on Glasgow's 29 secondary schools, they involve local primaries and pre-five centres planning for children's needs on an areas basis along with professionals from other agencies.