The guidelines are to be published next Tuesday in a booklet funded by the Calouste Gulbenkian Foundation and produced by the British Association for Counselling and Psychotherapy, which has received a rising number of enquiries from teachers and authorities.
Counselling has now gained recognition as "a valuable early intervention and preventative strategy to stop any deterioration in the mental health of children who have emotional and behavioural problems", the booklet states.
The guidelines can be used in working with troubled children as young as three. They are intended for youngsters whose problems manifest themselves through disruptive behaviour or being withdrawn as they "bottle up" their fears and worries.
The booklet is a Scottish edition of one published in England last year. It was edited by Janette Newton, chair of the expert group Counselling in Education, the UK's only team of school counsellors, employed by Dudley education authority in the Midlands.
The move has the backing of the Headteachers' Association of Scotland. Mike Doig, its president, said: "As a nation famous for its emotional illiteracy, we need to examine our mechanisms for identifying and responding to social and emotional problems in pupils - and to recognise the increasing value of professional counselling."
Counselling may also have a role to play with truants. "There is a clear link between poor attendance and anti-social behaviour. Ironically efforts to improve attendance by setting government targets serve only to increase the pressure on those involved," Mr Doig said.
He also believes that a professional counselling service could counter the fall in the number of guidance teachers post-McCrone. "External counsellors could help us fill this vacuum from the start. There is no doubt that demand for their services will expand significantly in the coming months," Mr Doig said.
The booklet assumes that counselling skills can be used by teachers and this was supported by Gwynedd Lloyd, senior lecturer in educational support at Edinburgh University's School of Education.
"Many children would rather speak to someone they know than to a professional who is a stranger to them," Dr Lloyd said. "But schools have to make clear what their policy on confidentiality is."