The new survey will cause concern in the United States where the current trend is to create smaller schools. The report suggests that while small schools offer superior learning conditions they may be a poorer environment for nurturing pupils' emotional development.
The study of 13,000 eight to 13-year-olds, published in the academic journal Sociology of Education, confounds prevailing wisdom that small schools - typically serving fewer than 400 pupils at primary level and no more than 800 at the secondary - make for happier students, greater sense of community and teachers better able to spot troubled youngsters.
"I was very surprised," said Toni Watt, assistant sociology professor at Texas State. "There was a great deal of research that small schools are better academically, but only anecdotal evidence they are emotionally. When I did the study I expected to be offering empirical evidence (to back that up)."
Small schools may be "more homogeneous and cliquey", alienating some students, unlike larger schools with broader social spectrums, said Ms Watt, who compared them to small towns "where everyone knows your business and every infraction is visible". Small school proponents said the survey could have been skewed by the disproportionate number of disturbed students small schools serve.
"It's like saying hospital has higher rates of sick people," said Michael Klonsky, education professor and director of the Small Schools Workshop at the University of Illinois at Chicago.
But Ms Watt said she made allowances for students with psychiatric histories predating attendance at a small school to try to rule out this factor. "There are a lot of people upset about my study," she conceded. "It doesn't mean small schools are bad though. At best it means there might be some unmet needs."
Mr Klonsky, however, said the findings were at odds with his own that violent incidents at schools with more than 700 pupils outstripped tenfold those at schools with fewer than 300.
Some 130 out of Chicago's 650 state schools are now small, estimated Mr Klonsky, and New York plans to open 200 small schools in the next two years. This reflects a trend sweeping American public education since the turn of the 1990s towards carving up sprawling campuses into so-called "learning communities," also dubbed "multiplex schools".
This represents a dramatic shift from the preceding 50 years when bigger was better with America's 200,000 state schools being consolidated into 62,037, driven by notions that large schools, offering broader curricula, were optimal.