A report by the Education Policy Institute found that 10.1 per cent of children who finished their GCSEs in 2017 experienced exits at some point during their time at secondary school that "cannot be accounted for".
This totals more than 69,000 unexplained exits by over 61,000 pupils - higher than the 2014 proportion of nine per cent.
The study builds on previous EPI research published in April. The think tank said the latest research provides the most refined estimate to date of the potential size of so-called "off-rolling" in the school system - the practice of schools informally removing pupils, in order to boost GCSE results or to manage pressures on special educational needs and disability (SEND) and other budgets.
It also reveals which local authorities and multi-academy trusts have the highest rates of unexplained exits in their schools.
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It found very high rates of unexplained pupil exits from schools among several local authorities and multi-academy trusts (MATs) in England.
While there is not a large difference between MATs and local authorities in rates of unexplained exits, overall, larger MATs have above average rates.
In more than a dozen school groups, a pupil is at least twice as likely to experience an unexplained exit than the average, with those in the highest school group six times as likely.
The report calls for better data, monitoring and transparency around pupil moves in the school system, and urges the government to improve guidance given to schools, so that it genuinely recognises the complex causes of pupils' behavioural difficulties, and offers schools clear information and training on their responsibility to support pupils with SEND.
It also wants school performance and accountability measures to take account of the vulnerability of pupil intakes, and reward more inclusive schools. It says the government's review of high needs funding should consider implementing a funding allocation system that promotes inclusion and early support for children with SEND.
Jo Hutchinson, report author and director of social mobility and Vulnerable Learners at the Education Policy Institute, said: "This research shows that there are thousands of pupils in England routinely removed from schools with no apparent explanation. While certain groups of schools display very high rates of pupil exits, it is also clear that this phenomenon pervades the entire school system, and requires intervention at a national level.
"The overwhelming majority of exits from school rolls are experienced by more vulnerable pupils, such as those with special educational needs and disabilities. The government should reduce perverse incentives for schools and do more to promote inclusion - only then will it help to prevent those with more complex needs from being moved around the system".
Dr Mary Bousted, joint general secretary of the National Education Union, which sponsored the study, said it "lays bare the facts of off-rolling".
She said: "Sixty-nine thousand unexplained pupil exits from schools is a shocking figure and one which the government needs to address. That pupils with complex needs are most likely to fall out of the school system shows that as a country we are failing our most vulnerable children.
"The reasons are complex, and providing guidance or policing schools will not solve the issue. Funding cuts to local authority support services and access to child mental health services are also making an impact on a school's ability to support children most in need."
Last month, Ofsted revealed that the number of schools suspected of off-rolling has risen by 13 per cent in a year. Chief inspector Amanda Spielman has previously called for action on the issue.
Following Edward Timpson's review of exclusions, the government has vowed to make schools accountable for excluded pupils and close loopholes used to off-roll.
A Department for Education spokesperson said: "While we back head teachers in having robust behaviour policies and to use permanent exclusions as a last resort, we are clear that it is against the law to remove pupils on the basis of academic results. Any school that does this is simply breaking the law, but unexplained pupil exits is not the same as off-rolling.
"As this report highlights, the increase in unexplained exits is small and there are not large differences between exits in multi-academy trusts and local authorities, and we will continue to work with Ofsted to tackle off-rolling in any setting."
