The report, released last month, profiled schools in Gauteng, Limpopo and Eastern Cape.
Poor quality infrastructure, poorly qualified teachers and the difficulties encountered by pupils in schools were among the key areas identified.
The Department of Basic Education, however, questioned the report, saying it could not be used as a measure of the quality of education in the country, but rather as a sample of some rural schools.
The report found that, although South Africa has done a lot to improve access to education, the system continues to be hampered by strong historical inequalities that do not were not effectively fought by the government.
According to the report, a child's educational experience always depended on his place of birth, the wealth of his family and his race.
He revealed that more than three-quarters of 9-year-olds could not read meaning in some provinces. Out of a total of 100 students entering school, 50 to 60 would pass the program, 40 to 50 would pass the program and only 14 would go to university.
The report also pointed to infrastructure problems, saying that some schools had poorly maintained buildings that had never been renovated. Other buildings contained hazardous materials, including asbestos.
The safety of students and staff was also mentioned in the report, with one school being burgled once a month and another being burgled 10 times a year.
There is a need to improve student transport systems to school as many students walk to school, according to the report.
There were also problems inside the classroom, such as overcrowding.
Teachers expressed concern about the multiple changes to the curriculum. Support for teachers is often lacking, with insufficient professional development and commitment on the part of pedagogical advisers, read the report.
The skills of thousands of teachers in specialized fields, such as math and science, were questionable, as they were neither qualified nor underqualified.
A study carried out in March 2018 found that South African teachers could not take simple math and English tests, with some scores as low as 10% for English as an additional first language and 5% for math, according to the report.
The report recommended a review of teacher training.
Basic education spokesperson Elijah Mhlanga said the department was disappointed with the report, saying it was dotted with inaccuracies, its data had been out of date and some of the issues raised had already been dealt with by the department.
You can't use a few out of 25,000 schools and say it's a national picture. You can't, said Mhlanga.
He said they would meet with the organization to resolve some of the problems identified in the report.
The director of the School of Education Studies at the University of KwaZulu-Natal, Professor Labby Ramrathan, said that there were two school systems in the country, one for the poor and one for the poor. Other for the wealthy.
Infrastructure needs to improve and all stakeholders need to be involved in education. Parents should encourage the culture of learning in their children, and classroom teachers should teach. These are just a few of the things that need to happen, otherwise we will be talking about the state of education over the next 20 years, he said.
National Teachers Union president Allen Thomson said the report needs further investigation.
There are certain things with which we agree and others with which we do not agree.
Secretary General of the Democratic Teachers Union, Mugwena Maluleke, said the education system was not broken, but uneven.
He said that a poor school background and infrastructure affected the self-esteem of students from poor communities, and this affected their progress.
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