The six-year study, involving 3,000 schools in 73 local education authorities, was led by Pat Preedy, head of Knowle Church of England Primary School in Solihull, West Midlands.
The question of separation in class was found to be a common cause of conflict between teachers and parents.
Mrs Preedy embarked on the research when the number of twins in her classes jumped from one set to 10 pairs.
The study sample consisted of 619,633 pupils, of which 11,873 were twin children with 117 sets of triplets and five sets of quads.
The survey found that only 1% of primary schools had a relevant written policy.
Parental choice
Some teaching staff thought that separation was beneficial for individual development while others felt that twins should be kept together as a natural unit.
Mrs Preedy told BBC News Online: "Decisions are frequently based on assumptions.
"Sometimes opinions were just what a member of staff had heard somewhere or read in a newspaper."
Those which kept children together said this was to allow them to support each other, because of the wishes of parents, or simply because there were no apparent problems or reasons for separation.
Schools with classes grouped alphabetically or by birth date often automatically placed twins together without considering the effects.
No discussion
Mrs Preedy said that more than three quarters of schools questioned did not discuss this issue with parents.
"The steady increase in multiple births heightens the need for increased awareness of the special consideration required in managing the children's progress," she said.
One child in 35 is now a twin, triplet or quad, according to the survey.
The national increase is partly a result of fertility treatments - particularly the incidence of triplets.
Better neo-natal care has led to a higher survival rate for small or premature babies.
There has also been a trend towards older motherhood when twins are more likely.
Mrs Preedy, who is educational research consultant for the Twins and Multiple Births Association (Tamba), said that there are no clear-cut answers.
Flexibility advised
She recommends schools take a flexible approach in each case and conduct regular reviews.
"We are not saying there are huge problems but you need to watch for extremes and see if children need help to behave, and be treated, both as individuals and as twins or triplets," said Mrs Preedy.
Her study concluded that some children need to be together at the start of their schooling to support each other, particularly as 84% of those surveyed had previously spent very little time apart.
"Others wanted to be separated or they started off together and then separated later."
Types of twin
Mrs Preedy places twins in three categories:
"The main issue is not so much whether to separate children but how to help them develop as 'mature dependents'," she said.
"These children enjoy their multiple-birth relationship but are able to choose some things the same as their twin and some things that are different.
"They are able to develop as individuals, making their own friends and accepting that they cannot always be the same as their twin."
Framework policy
The results of the study are included on a website in a joint initiative with Professor David Hay of the University of Curtin in Australia.
He leads specialist research into the educational and social needs of multiple-birth children.
Mrs Preedy, whose study has been conducted through the University of Birmingham, has drawn up a framework school policy and parent/teacher questionnaire.
She has also devised a theoretical model to assist professionals in the personal, social and emotional assessment of the children.