Bruce Adamson called on both institutions to ensure the uncertainty around the exams will not lead to children being disadvantaged.
He said any appeals system created by the SQA must also be human rights compliant and available to all children, free of charge.
The Scottish Government and the SQA were criticised in the review of the exam results fiasco undertaken by Professor Mark Priestley on the issue of appeals, with leading children’s rights academic Dr Tracy Kirk writing in the Scotland on Sunday this week the same mistakes must not happen again.
Mr Adamson said the SQA must “urgently communicate” their plans for the alternative certification model for 2021 Highers and Advanced Highers and “anticipate” disadvantage pupils were likely to experience.
The children and young person’s commissioner said: “Young people have had varied reactions to the news that exams would again be cancelled. For some, this is a relief, but for others, particularly those who were negatively affected by the cancellation of the previous exam diet, it has increased stress.
“The Scottish Government has a duty to ensure that children and young people can realise their human right to education. The SQA in its most recent Child Rights Impact Assessment recognises that the right to education requires the provision of appropriate assessment arrangements.
“The SQA must urgently communicate what their alternative assessment arrangements will be for pupils due to sit their Highers and Advanced Highers in 2021. Uncertainty has created a huge amount of anxiety and stress this year for young people.”
He said that an appeals process must be created that is free to access and directly available, without the involvement of schools.
In 2020, schools were required to sign off on any appeal, even if it was due to alleged discrimination of the pupil.
Mr Adamson said: “The alternative assessment system will be untested, so the SQA must anticipate that some young people will experience disadvantage and must ensure they have access to remedy through a direct appeals process.
"The appeals process needs to be human rights compliant, robust and take into consideration the needs of all young people.
“I’m calling for the SQA to make direct appeals available to young people, at no cost, for the 2021 National Qualifications results.
"This should include the ability to dispute a teacher or centre estimated grade and to challenge a failure to make reasonable adjustments, as required under the Equality Act 2010.”
In response, the SQA said it would announce the details of the replacement for the exams “shortly” and that it was “committed” to working with the commissioner and others to develop an appeals system that “fully respects” children’s rights.
A spokesman said: “As outlined last week, SQA is co-ordinating the development of an equality impact assessment as part of a quality assurance model, which aims to ensure fair and credible results for all learners.
"Schools, colleges, local authorities and SQA are committed to working together to support teachers and lecturers in providing their provisional results in a fair and equitable way in 2020/21.”
The Scottish Government said:
A Scottish Government spokesperson said: “The SQA will be providing guidance on the alternative arrangements for Higher and Advanced Higher certification as a matter of urgency. This work has been set out for National 5.
“In light of Professor Mark Priestley’s independent review into the events following the cancellation of the 2020 exams, we have asked the SQA to review their appeals system from 2021 to ensure it best meets the needs of young people in line with the principles of the United Nations Convention on the Rights of the Child.
“That review involves working closely with key stakeholders, including learners and their representative groups, as well as the Children’s Commissioner. Full details of the SQA appeals process for 2021 will be set out in due course.”