The figures from the census of all schools in England provide the first complete picture of what is happening in the independent sector after the new 20% VAT on fees was introduced at the beginning of the year.
Overall, 582,477 pupils in England attended private schools when the census data was collected in January this year, down from 593,486 the year before - a drop of 1.9% (or 11,009 pupils).
Overall pupil numbers in England have fallen slightly to just over nine million. There was a smaller drop (0.6%) in the number of pupils not at private school.
Private school pupils now make up 6.4% of the total school population, a slightly lower proportion than last year, when it was 6.5%. This is the first time since the Covid-19 pandemic that independent school pupil numbers have fallen.
The government had previously predicted that around 3,000 private school pupils would need to be absorbed into the state system this academic year, with state school places needed for around 37,000 private school pupils over the coming years.
This was an estimate of those who would be motivated to take their children out of private school as a direct result of its decision to remove the VAT exemption from private school fees, not taking into account any demographic changes.
The census data does not give clear reasons as to why pupils have left private school.
It could include a shift in international students or a move to home-schooling which would not be reflected in the state school figures.
Julie Robinson, chief executive of the Independent Schools Council (ISC), a body which represents most of the private schools in the UK, suggested that VAT on fees was putting pressure on parents and was the reason behind the drop.
She said: "More pupils have left than the government's own estimates. This outsized exodus should concern anyone who is interested in this tax on education as a revenue raiser."
The ISC, which represents more than 1,400 private schools, previously said its annual census showed average school fees were 22.6% higher in January 2025 than they had been in January 2024.