More than 30,000 children were missing from schools in England and Wales for substantial periods of time in the 2014-15 academic year, local education authority figures show.
Of these, almost 4,000 children could not be traced by the authorities.
The National Children's Bureau said some may be at "serious risk" of abuse and exploitation, including forced marriage, FGM and radicalisation.
The Department for Education said it had issued "new guidance" to schools.
Ofsted has previously raised concerns that some missing children could be hidden away in unregistered, illegal schools.
The figures, obtained by the BBC's Victoria Derbyshire programme, show that 33,262 school-aged children were recorded as missing from education in the academic year ending in July 2015. They were collated from a Freedom of Information request to 90 local education authorities in England and Wales.
Children were recorded as "missing from education" if they were of compulsory school age, and the authorities were unable to trace them - typically for four weeks or more, or two to three days in the case of vulnerable children.
More than 10% of these children - 3,897 - could not be traced by local authorities.
Manchester recorded the highest figure - 1,243 children were missing from education, including 810 children whose whereabouts were unknown in July 2015.
In Bradford 985 school-aged children were missing - the authority was unable to trace 321 of them after "extensive enquires".
In some cases, children were recorded as missing because they had moved out of the area, or gone abroad, and their parent or guardian had failed to tell the school. However, in most cases where a child had been traced, local authorities could not give a reason why they had disappeared.
"When I was 15, my dad thrust a picture of my cousin towards me and said, 'This is who you're going to marry'.
"I didn't know what to say, I was scared. The only thing I could think to do was run away from home, but my brother found me."
Zainab - not her real name - says that from then on, she was, in effect, a prisoner in her own home.
"I was pulled out of school, I wasn't able to finish my GCSEs. The school did send two letters home to my dad. But he just chose to completely ignore them.
"And then we moved house, and the school didn't know. I was completely off the radar."
After seven months of being locked inside, Zainab managed to call a charity from her brother's phone.
The National Children's Bureau believes there are a number of "very serious risks" with children going missing.
Enver Solomon from the charity said: "Some councils do a fantastic job, but unfortunately some councils don't do a good enough job by any stretch of the imagination.
"There shouldn't be one child in the country who isn't in school and can't be tracked, because of the potential risks.
'We know [of some] horrendous cases, of sexual exploitation. We also know about the correlation between missing children and the possibility that they may be involved in forced marriage, and of course, issues relating to young people's involvement in extremist activity."
The charity - as well as other child protection agencies - said the figures were likely to underestimate the scale of the problem.
Children can easily disappear from education without being reported, it said, because families may tell a plausible story to the school - like they are home-schooling or going abroad.
In response to the figures, a spokesman for the Department for Education said: 'We have issued new guidance to local authorities and schools making clear that they have a duty to establish the identities of children who are not registered at a school or receiving a suitable education.
"Where children are being put at risk, local authorities and the police have clear powers to take action."
The Victoria Derbyshire programme is broadcast on weekdays between 09:00 and 11:00 on BBC Two and the BBC News Channel.