Grades of schoolchildren whose exams were cancelled will be determined without consulting their teachers.
The Scottish Qualifications Authority, which it was claimed could also penalise students at schools in deprived areas, said there was not enough time to enter dialogue with every school or college.
Moderators, the agency said, faced a tight deadline to deliver grades on August 4 to thousand of candidates across Scotland unable to sit exams because of lockdown.
It previously admitted pupils’ grades could be affected by the performance of their school in earlier years.
Scottish Greens education spokesman Ross Greer said: “The SQA are undermining not only the professional judgement of teachers but the hard work of pupils with this secret moderation process.
“They are treating young people as statistics, not as individual learners.
They are treating young people as statistics, not as individual learners.”
Ross Greer, Scottish Greens
“Applying a system that penalises pupils who go to schools in deprived communities is bad enough, but to do so in secret is utterly unacceptable.
“Teachers will now be faced with having to understand for themselves why the grade they submitted has been altered, as well as the methodology of the system used to alter it, all just days before schools return for the new term and with a huge volume of additional work expected of them if they and their pupil wish to appeal the SQA’s decision.”
The Scottish Parliament’s education committee previously asked the agency to speak with schools and colleges where there was a difference between this year’s estimates and historical attainment data.
In a letter to the committee this week SQA chief executive Fiona Robertson said: “We have considered the matter very carefully, including further discussions with our board of management and we have concluded that it will not be possible to include engagement with schools and colleges within the moderation process.”
She said it would be difficult to operate dialogue fair and consistent in treatment of all centres and candidates and impossible to do so in the very tight timescales between receiving estimates from schools on May 29 and finalising grades before July 10.
The appeals process would provide further evidence-based consideration of grades which schools or colleges think are unfair, Ms Robertson said.
An SQA spokesman said: “We have published guidance and information on our approach to certification this year.
“Further information will be provided on August 4. Fairness is at the heart of our approach.”