The Examinations Appeals Board is recommending a review of procedures at the Edexcel and OCR boards after finding "totally unacceptable" mistakes.
The criticisms come after several cases in which students waited a year or more to have appeals against grading decisions heard, following repeated administrative errors by the boards.
The EAB rejected complaints from three schools about marking procedures, saying they had been sound, but expressed serious concerns about the amount of time it took to process appeals.
The EAB, which is the last recourse for students who appeal, said that the "whole area of inquiries and appeals" should be reviewed by the Qualifications and Curriculum Authority and Joint Council for General Qualifications. It also proposed changes to the exams code of practice.
In the first case, Trinity Catholic high school, in Redbridge, Essex, complained to Edexcel in August 2002 on behalf of a biology and chemistry A-level student.
The school was still not happy when papers were re-marked, and appealed again. It took Edexcel until May this year to say it would not hear the appeal.
The EAB told Edexcel it should hear the appeal when the school complained.
The appeal then took place in July this year but the school lost. However, in the meantime, the board had destroyed one of the candidate's papers. The EAB also highlighted communication problems between departments at Edexcel, and missed deadlines in replying to queries.
The EAB also commented on delays affecting a student from Ampleforth College, north Yorkshire, who had appealed to OCR over a 2002 A-level history grade.
The appeal took more than a year to hear and the EAB said the school had also been misled by the board about the appeals process.
Merchant Taylors' school, in Northwood, north London, complained to the EAB about marking mistakes and administrative problems affecting 18 AS Latin students.
The school complained about "insulting comments", including "cor" and "blah" written on two scripts by an examiner. Photocopies of some scripts returned to it by OCR were "barely legible" and delays in the appeal process meant it took 15 months for some queries to be answered.
OCR and Edexcel both accepted that some of their administrative systems had not operated perfectly, OCR adding that it was sorry for the difficulties.
Both boards said they had made big improvements in handling appeals this year. The QCA and JCGQ said they were keeping the situation under review.