This will inevitably fuel fears in colleges that they will be used as a "dumping ground" for pupils when schools cannot cope.
The guidance, published yesterday (Thursday), suggests such pupils could attend college full-time even if they are below the leaving age.
Tucked away in an annex, the Scottish Executive document states: "College courses may deliver an alternative curriculum for those pupils who have become disaffected with their education and are on the verge of exclusion.
"These programmes can offer a lifeline to pupils who have switched off from their school courses and may be proving disruptive, be involved in truanting from school or become established as a non-participator."
The guidance states that such pupils could be victims of bullying which might lead them to stay away from school, posing the risk that they will be excluded. "In these cases, colleges can help by discussing the issues with all parties involved and, if appropriate, prepare a full-time timetable for the pupil," it states.
Other youngsters who could come knocking on college doors include pupils who have committed offences and are in secure accommodation awaiting release, and those who have been sexually assaulted and for whom a college may be the best option.
The document suggests that educating such pupils could be a time-consuming business. It emphasises that colleges which enrol students on a full-time basis will require the agreement of the pupil, the school's headteacher, parent or carer, the local authority, education psychologists and social workers.
"It is important that all involved in the welfare and support of the pupil work closely together and share information to assist in the delivery of a quality learning experience for them," the document states.
It sets out a "model partnership agreement" to which all involved in school-college collaboration would be expected to sign up. This details the responsibilities of the college and the school and local authority.
There is also a model student agreement that commits pupils to certain standards, such as good behaviour and discipline. The threat for those who fall short, the document suggests, is a return to school and removal from their college programme.
Ministers have been at pains to emphasise that they do not want the arrival of many more school pupils to lead to changes in the adult and vocational environment in FE.
The key ethos of colleges as voluntary learning centres for adults is their distinctive contribution and must not be altered, Jim Wallace, Lifelong Learning Minister, said at the launch of the strategy in Edinburgh's Telford College.
It is clear none the less that colleges will have to adopt a number of school practices such as parents' evenings, providing an annual progress report and taking a class attendance register.
College staff teaching school pupils will also have to possess or be working towards a teaching qualification, "or have other means to demonstrate that they can teach to the requisite standard". This is an attempt to balance the competing demands of schools where all teachers have to be qualified and of colleges where they do not.
Another implication for colleges is that they will have to come to terms with the several pieces of legislation affecting pupils, such as the Standards in Scotland's Schools Act, data sharing, and disclosure checks for those working with the under-18s (though adult students are generally exempt where they are learning alongside under-18s).