The Scottish Council of Independent Schools says there are 31,146 pupils in the sector - the lowest figure since 2003.
Its figures also reveal a 2.9% decline in overall numbers since a 10-year high in 2007, when there were 32,065 fee-paying pupils.
The decline has been most marked in the primary sector, where pupil numbers have dropped by nearly 7% from 13,450 in 2007 to 12,527 this year.
Concern over the impact of the economic downturn on the ability of families to afford private school fees has been a key topic for the sector in recent years.
Many schools have kept fee increases to a minimum as parents grapple with the downturn, but the average cost rose 4% this year, making average annual fees £12,500. The increases mean a significant additional burden for families for whom school fees are on the margins of affordability.
A Bank of Scotland report published before the impact of the credit crunch warned some Scottish professionals could no longer afford to send children to fee-paying schools, with teachers, engineers and police officers priced out of private education.
However, the Scottish Council Of Independent Schools (Scis) says figures have remained relatively stable over the past decade despite the impact of the recession, suggesting high levels of confidence parents have in independent schools.
Another factor in the maintenance of numbers is the means-tested financial assistance independent schools distribute to widen access, with some £35 million awarded in recent years to families unable to afford the full fees.
John Edward, director of Scis, said: "Any parent who pays school fees will confirm the outlay is worthwhile if their children are happy at school, and this is undoubtedly a key reason pupil numbers in our sector have remained stable, alongside the financial assistance that schools allocate to widen access."
Mr Edward also said boarding schools had seen a recent rise in the number of enquiries following the launch of a Scis website to highlight opportunities in Scotland.
Independent schools educate 4.5% of the total pupil population in Scotland. They also attract international students from countries such as Germany, China, Russia, Hong Kong, Spain, North America, South Asia, France and Nigeria.