Research commissioned by the Children's Legal Centre shows the system is so complicated that it can be impossible for parents to get their children into schools.
Voluntary workers believe hundreds of children in some areas are not in schools despite claims by local councils that there is no problem.
Yvonne Spencer, head of practice at the centre, said even the Home Office did not know how many asylum-seeking and refugee children should be in school.
Anecdotal evidence suggested that children aged 15 or more were particularly at risk of missing out on school.
"Many (local education authorities) take the view that they are leaving within 18 months so they won't provide anything for them," said Ms Spencer.
"These children, if given leave to remain, won't be educated, won't be able to join the workforce and will be at risk of criminal offending or exploitation such as prostitution."
The Home Office said groups had been established to look at the education of refugee children.