Thousands of pupils from leading state and independent schools across Scotland were apparently given artificially inflated exam qualifications through a controversial computerised appeal system.

Under the scheme, which was scrapped last year, Standard Grade and Higher exam results at certain schools were automatically upgraded without being separately checked by officials at the Scottish Qualifications Authority.

New SQA figures reveal that in 2007, when these exam appeals - thought to number about 10,000 - were manually checked for the first time in 15 years, a large proportion were rejected. That led to the successful proportion falling by 4% for Highers and 2.6% for Standard Grades, demonstrating that a sizeable number of previous upgrades were questionable.

The automatic system, known as derived grades, was available only to schools with significant numbers of pupils sitting exams, meaning it favoured larger independents and comprehensives in wealthy suburbs, as opposed to those in deprived or sparsely populated areas.

Last night, campaigners against derived grades, which included the SNP in opposition as well as teachers, said the figures proved the old system, introduced in the early 1990s by the former Scottish Exam Board, was unfair.

Christina McKelvie, SNP MSP and a member of the Scottish Parliament's education committee, said: "This change in the appeal rate shows the SNP was right to demand the end of the derived grades system which was seen to clearly favour pupils in better-off areas or in private education.

"Pupils, teachers, universities, and potential employers can now be confident that the grades shown on the certificate were earned properly and are the result of the effort put in by the pupil and the teachers."

John Milligan, a science teacher from Sutherland who was responsible for starting a campaign to end derived grades, said the figures vindicated his position.

"It was was already hard enough for pupils from poorer areas to overcome hurdles in their path and this system supported that. This shows how flawed the system was," he said.

Eleanor Conor, a spokeswoman for the Scottish Parent Teacher Council, added: "There were always concerns about the operation of derived grades. This shows it was right to scrap them."

Judith Sischy, from the Scottish Council of Independent Schools, said private schools had not reported a big drop in success last year.

"The general view from our discussions was that this has not made a particular difference," she said. "Having said that, we felt it was a system introduced a long time ago which was found to be inequitable because it favoured large schools."

However, a spokesman for the SQA said it was too early to draw definitive conclusions about what had influenced this year's appeals success rates.

"Work we have already carried out and published shows there are several factors that influence year-on-year changes in appeals success rates."

The derived grades system was axed after an internal SQA report suggested teachers could be over-estimating what their pupils would achieve in Standard Grades and Highers.

The procedure was triggered when pupils' results were out of line with expectations. After the exams were marked, pupils who had under-performed at schools where most pupils achieved their predicted grades were automatically upgraded. But to take part in the process, more than six pupils from every class had to have the same predicted grades in the same subjects.

Schools with small class sizes or those where only a handful of pupils were predicted A passes were not eligible. Therefore, bright pupils who just fail to meet their predicted grades from these schools would not be automatically uplifted.

Internal SQA research found independent schools were the main recipients of upgraded Highers, while state schools benefited the most from upgraded Standard Grades.

Five out of the 10 schools with the most derived grades were private, with George Watson's College in Edinburgh topping the list and Hutchesons' Grammar in Glasgow coming second.

Two comprehensive schools from East Renfrewshire, Williamwood High School in Clarkston and St Ninian's in Giffnock, also had a high number of derived grades.