It found that while most school-refusers and phobics have a combination of academic and social problems, home was where these most commonly originated.
However, many schools did not differentiate between the two conditions or have effective policies, the National Foundation for Educational Research said.
Reasons for non-attendance included concerns about school transfer, lessons or particular teachers, fear of bullying, academic pressures and friend problems.
Usually, however, these issues had arisen because of earlier trauma at home. These included family break-up or bereavement, abuse, or where a child was responsible for caring for a relative.
The study of 60 education authorities and a sample of 600 schools, showed that boys and girls were equally affected, usually during their secondary years and that they usually came from deprived or dysfunctional homes.
But schools admitted they had little training on how to deal with school refusal and phobia.
Where there was effective support it often came from special units, where teachers were better trained and were able to provide a safe haven outside the normal school buildings, as well as individual help with their work.
The report found early detection was important to prevent the cycle of non-attendance which fuelled other problems, such as losing contact with friends, and made it difficult for the child to return.
School phobia and school refusal: research into causes and remedies, pound;8, is available from the NFER on 01753 637002 or firstname.lastname@example.org Matt Buck's Education week 35