The figures released yesterday would be lower were it not for record numbers of foreign pupils in boarding schools.
They show that about 7 per cent of pupils are in independent schools, the same proportion as in 1986-87 when parents were escaping from the disruption caused by teachers' strikes.
The schools say the fall in numbers is low, given the recession.
Last year, total numbers fell by just under 1 per cent compared with 1.5 per cent the previous year, despite an overall rise in the school population, according to the annual survey of the Independent Schools Information Service.
Boarding was down by 5.2 per cent compared with a drop of 6.2 per cent in the previous year. There was a rise of 0.1 per cent in day pupils. Pupils from overseas, mainly Europe and the Far East, increased by 10 per cent, bringing pounds 150m in foreign currency and more than offsetting the drop in children from armed-services families.
The survey records the lowest annual fees increase since the census began in 1982 - 2.6 per cent - compared with 8.3 per cent the previous year and 12 per cent in each of the two years before that. The estimated rise for September is about 4 per cent.
David Woodhead, director of ISIS, said: 'The improvement in day numbers and the slowdown in boarding's decline indicates a more rapid recovery from a much worse recession compared with the early 1980s. 'Whether the recovery in numbers continues depends on how much the tax increases which have just been introduced affect parents' disposable income.'
Head teachers say parents are moving their children between state and independent schools in an unprecedented way. Brian Maybee, head of the Mount School, Bromsgrove, said he had this year received more eight- and nine-year-olds from state schools than at any time for a decade. However, more of his 11- year-olds were going into state schools than before.
The survey says that the increases in fees have been necessary to meet rising teachers' salaries, which account for 80 per cent of costs in day schools and 60 per cent in boarding schools. It points out that education costs are always ahead of the Retail Price Index.
Leading article, page 17