More than 55,000 children have been moved out of school - and in a small number of schools with very high rates, the equivalent of an entire classroom of pupils have left in this way over five years, between 2012 and 2017.
The research, carried out by the Education Policy Institute (EPI) think-tank, found that pupils with certain characteristics are disproportionately represented: one in three pupils were in the social care system, one in seven were disadvantaged, and one in eight were black.
The report, Unexplained pupil exits from schools: A growing problem?: A growing problem?, which looked at pupils who moved schools for reasons other than a formal exclusion or a decision made by parents, found that almost a quarter of the moves have taken place in 330 secondary schools.
It also reports that more than eight per cent of the cohort that finished year 11 in 2017 were subject to an unexplained exit.
Commissioned by the National Education Union, the EPI looked at more than a decade's worth of Department for Education data, to improve the nation's grasp of "off rolling" - where schools informally remove pupils in order to boost results, or for other reasons.
It is widely claimed that this practice has developed as a way of dealing with more challenging pupils, such as those with special educational needs.
It follows a string of warnings from the sector, including by Ofsted, the Children's Commissioner for England, and the Association of Directors of Children's Services.
The researchers said the report is being published as a working paper, with an open consultation on the methodology used.
Jo Hutchinson, report author and director of social mobility and vulnerable learners at EPI, said: "This research provides important evidence on unexplained pupil exits in the school system, following reports of children being removed by schools for reasons that are not in the pupil's best interests.
"For the first time, we begin to see the full scale of this problem, having stripped away cases where family decisions have led to school moves.
David Laws, chairman of the think-tank and a former education minister, said: "The size of unexplained pupil moves is disturbing and will raise concerns about whether some schools are 'off rolling' pupils.
"We need to look particularly closely at the six per cent of schools which account for almost a quarter of unexplained moves."
The EPI said further research would be published in the near future, shedding further light on local trends.