Robert Gordon's College in Aberdeen has raised #163;1.35 million since 1996, half of which will go towards underwriting places.
Similarly, Mary Erskine School and Stewart's Melville College in Edinburgh is benefiting from an unexpected legacy of #163;4.8 million. Interest of #163;300,000 a year is subsidising places for 20 pupils.
Figures compiled by the Scottish Council of Independent Schools show 31, 585 pupils attending member schools this session, a fall of only 171 pupils or 0.5 per cent on last year. Boarding pupils are down again to 4,044, a fall of 230 or 5.3 per cent on 1997-98.
Rose Bell of the Independent Schools Information Service said: "It does not look as though the effect of the assisted places is showing up as yet."It will be another six years before the #163;14 million scheme is phased out altogether. No new applications were accepted this year.
The total number of children currently on assisted places is 3,237, around 12 per cent of the total in independent primaries and secondaries.
Brian Lockhart, head of Robert Gordon's, said numbers are up, although the school has lost 12 assisted places. Eighty of 1,400 pupils are on the scheme. Almost a quarter of pupils are given help from a number of sources.
Mr Lockhart said: "Governors have had to find #163;50,000 this year. If all the assisted places pupils dropped out, we are talking large sums of money. The real test will come down the line in three or four years."
With fees at #163;4,500 a year, the school would lose #163;360,000. An appeal launched two years ago, anticipating the demise of the scheme, has so far raised almost #163;700,000 to subsidise places, some of which has been used this session. "We are obviously coping," Mr Lockhart said.
Bryan Lewis, vice-principal of Mary Erskine and Stewart's Melville, said both schools have never had so many applications, while the #163;4.8 million legacy allowed them to offer some pupils full fee support. But families have to reveal income and capital value to qualify. The assisted places scheme only considered income.
At Hutchesons' Grammar School, Glasgow, Sandy Strang, the depute rector, said "applications remained buoyantly high" because of the school's reputation. But he regretted the loss of support for families who could not afford fees of #163;4,000 a year. In an average year, 25 pupils would have joined through the assisted places scheme.
"Hutchesons' has prided itself on a social A to Z in line with the founders. It is not where you have come from, but where you are going to that matters, " Mr Strang said. The school is currently targeting parents and former pupils to raise funds to "redress the imbalance".
Juliet Austin, head of Kilgraston School, Bridge of Earn, said: "Our numbers are a bit down this year but we anticipated that. There are a number of children who would have come to us who now can't. We will have to market a bit harder and work a bit harder to provide assistance."
Mrs Austin said it was particularly tough on younger pupils who would be unable to follow their sisters into the senior school. One girl has been forced to leave for her local primary since the assisted places subsidy ends at primary 6. The girl would therefore have two major changes of school in two years.
Tom Ralph, bursar at St Aloysius' College, Glasgow, said the school was again oversubscribed. "In previous years we have had 30 kids on assisted places. This year it is 15 on some kind of bursary. We have probably experienced a slight shift in the mix of kids. Those from poorer areas probably won't come," Mr Ralph said.
Frank Gerstenberg, head of George Watson's College, Edinburgh, held back 15 places for support by the new school foundation. In previous years, 30-35 pupils in the first year were funded through assisted places.