GCSE and A-level results changed for 45,500 on appeal
More than 45,000 exam grades from this summer have been changed after schools challenged the results, up by 15%.
The number of inquiries questioning GCSE and A-level grades rose even more sharply, up by 48% to 450,500, according to exam watchdog Ofqual.
"Every such change has a big impact on the individuals affected," said education minister Nick Gibb.
"There is a growing lack of confidence in the exam system," said head teachers' leader Brian Lightman.
School leaders have voiced concerns about the quality of marking this summer - and the figures from Ofqual, for England, Wales and Northern Ireland, show a big increase in inquiries to the "review of marking service", up by 56% to almost 444,000.
There were warnings that mistakes in marking could mean that young people missed out on university places or being able to stay on to take A-levels.
Overall, about one in every 33 scripts marked this year resulted in an inquiry about marking or grades.
If schools and parents are not satisfied by the response to this inquiry, they can make a further appeal, and about one in five of these challenges resulted in a grade being changed.
This meant 45,500 grades have been corrected - up by 15% compared with the results of summer 2013. It represents a much bigger increase over the last few years - about 50% more grade changes than 2011.
"We're not surprised to hear that there has been a significant increase in requests for re-marks. Many schools have told us of a worrying number of results which simply did not reflect how well students should have done," said Mr Lightman, general secretary of the Association of School and College Leaders.
"Schools need to be able to trust the marks given to students. They need to know that examinations will be marked accurately, fairly and in a timely manner."
Mr Lightman said it remained unclear whether the increase in appeals is due to a "fundamental weaknesses in marking".
But he warned that the "lack of confidence in the exam system which has been exacerbated by frequent and ad hoc changes to qualifications".
The overall proportion of exam grades being changed remains low, but has increased for both A-levels and GCSEs. This year, 0.52% of GCSE grades and 0.65% of A-level grades have been changed.
Richard Harman, chairman of the Headmasters' and Headmistresses' Conference of independent schools, said: "We have been concerned about the accuracy of exam marking for many years, and so it is extremely worrying to see a new leap in the figures for re-grades this year."
"The college or university places of tens of thousands of students have been needlessly jeopardised this autumn and the exam boards must be made to do much better."
Education Minister Nick Gibb said: "It is essential that students can be confident that their hard work will be accurately assessed and the exams they sit properly marked.
"Parents, pupils and schools must have faith in exam marking and we are working closely with Ofqual and the exam boards to ensure this is the case."