The privacy of vulnerable children who leave mainstream education could be put at risk by a plan to store more of their data, a coalition of charities, academics and teachers has warned.

Sensitive reasons why a child may have left a school – such as physical or mental health issues, pregnancy or having committed a criminal offence – would be recorded under plans to expand a survey of those educated outside the mainstream school system.

The plan has caused concern among some in the sector who warn that the expansion of the so-called “alternative provision” census from January could lead to sensitive details being collected without the knowledge of parents and pupils. The Royal Mencap Society, the Alliance for Inclusive Education and the young offenders mentoring charity Trailblazers are among more than 20 organisations to put their names to the Defend Digital Me campaign demanding a rethink.

They say the information could be added to the national pupil database, which holds data on millions of pupils. They raise concerns that there are not enough safeguards to ensure that sensitive data does not end up being passed on to third parties and damaging the privacy of those it covers.

Officials insist that more information needs to be collected to ensure the reasons for pupils being sent to “alternative provision” are understood. They say there is a robust approvals panel charged with guarding the data, and that there are no plans to share the new information. Teenage pregnancies would not be recorded as a matter of course, they say, but pregnancy could be selected as an option explaining a placement. However, in a letter to the Observer, the coalition write that the new survey would “put school children in England at lifelong risk”.

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“The government must pause, rethink, and put children’s best interests first,” the letter states. “The Department for Education will collect reasons why children age 2-18 move from mainstream school into alternative provision education. Those sensitive reasons include a mental or physical health need, pregnancy, and whether a child moved to a young offender institution.

“These labels will be added to a child’s named record in the national pupil database, which now holds the confidential data of more than 23 million people without their knowledge or consent.”

Campaigners point to an audit of the use of NHS data in 2014 uncovered “significant lapses” in protecting patient confidentiality.

The letter comes amid increasing concerns about the number of children leaving the mainstream schools system, with both Ofsted chief Amanda Spielman and children’s commissioner Anne Longfield accusing schools of ridding themselves of difficult children to boost their results.

A recent report by the Institute for Public Policy Research thinktank warned that official figures on the number of children who had been excluded were “the tip of the iceberg”, and that five times more were being educated in schools for excluded pupils than official data suggests. Figures from the Department for Education show 6,685 pupils were permanently excluded from schools in England in 2015-16, most of them in the run-up to their GCSEs.

The coalition, which includes the Parents Union and Teenage Pregnancy Knowledge Exchange, warns that some data released to third parties from pupil databases since 2012 had been identifying. “New data protection law is in parliament, and while the government talk about giving children’s personal data special protections, and privacy by design, their actions do not,” the letter states. “We must see safeguards put in place to uphold children’s rights.

“We appreciate the importance of understanding these children’s education, often ‘managed out’ from mainstream school to boost league table results. But this knowledge should not cost any child their confidentiality.

“If the department cannot stop the distribution of identifying data for indirect purposes, and commit to the rights of the child, the government should not collect the data at all.”

A spokesman for the Department for Education said: “The reasons for a pupil being placed into alternative provision can be wide ranging. It is important that we understand these different reasons so we can ensure that we have an education system that works for all.

“The robust approvals panel and other controls are in place to ensure that this data, like all our data, is very safely guarded and only used in legal, secure and ethical ways.”