They are more likely to be unhappy at school, to miss time or be excluded and bullied. Children who are sexually exploited through prostitution will be experiencing severe family problems.
Ministers are now inviting schools to address the issues in a "non-stigmatising way" and asking education departments to work alongside other agencies in drawing up local protocols.
The Executive has flagged up existing initiatives such as the Scottish Anti-Bullying Network and the Scottish Schools Ethos Network in raising standards of behaviour in schools. It stresses, however, the value of health and social advice, including the role of new community schools.
Ministers suggest personal and social education programmes could be a vehicle for highlighting the circumstances surrounding running away and prostitution - if teachers are given "suitable materials to allow them to discuss these issues and to deal with any problems which may arise".
But PSE has its limitations, according to Alan McLean, a principal educational psychologist in Glasgow. "It lacks focus. What these children have in common is that they will be disaffected from learning. What they need is targeted interventions to re-engage them in their education," Mr McLean said.
He continued: "What can be surprising about girls involved in prostitution is that they are not acutely emotionally and behaviourally disturbed. They appear on the surface to be normal, although almost inevitably they are found to have experienced major family difficulties. Prostitution - and being exploited by an older man - becomes a form of learnt helplessness for them."
Gwynedd Lloyd, senior lecturer in special educational studies at Edinburgh University, said: "The key thing for vulnerable children is for them to have an adult they can trust and who will listen to them. Schools have not always been able to provide this."
She added: "The guidance system does not allow the time for teachers to provide the degree of individual attention these children need. And now post-McCrone even this system is uncertain."
The Executive is seeking views by the end of March on its suggestions, which include improved systems of support and advice for vulnerable young people, interviews with young runaways to establish the reasons for their behaviour and greater use of legal action against abusers.
Mr McLean said: "It is widely recognised that education is at the weaker - or softer - end of these multi-agency approaches. The biggest challenge of these approaches is to get social work and education to work constructively together."