The assessments measure literacy and numeracy in grades one to six. This year grade nine was added to the list.
The assessment results were released in a 72-page report by the basic education department on Monday morning.
"While not unexpected, the results for grade nine, particularly for mathematics, are a cause for great concern," Minister Angie Motshekga said at the formal release at Ipontshe Primary School in Tembisa.
There was an improvement in maths in all the grades that participated in the assessments, except grade six which decreased from 30% to 27%. There was a marked improvement from 28% to 41% in grade three.
The department's report stated, however, that the grade nine maths results were "below expectation" and will "receive the immediate attention of the DBE through additional and more intensive structured intervention programmes".
Head of the maths school at the Nelson Mandela Metropolitan University, Werner Olivier, said the grade nine maths results showed a "national crisis".
"It shows that we are on the brink of collapse in developing [technical] skills," he told the Mail & Guardian.
Lack of teachers
Many rural schools in the Eastern Cape lack maths teachers, for example, he said. "Every second school does not have a maths teacher.
"Something has to be done to assist learners without maths teachers."
Limpopo's grade nine pupils scored the worst with an average of 8.5%.
Only 2.3% of grade nine pupils across the country obtained at least 50% or more in the maths tests.
These results are "particularly worrying", lecturer in maths education at the University of the Witwatersrand, Lynn Bowie, told the M&G.
"This means there is nothing for pupils to build on for grades 10 to 12," she said.
Language results improved this year. The most notable improvement showed in the grade threes whose average mark increased from 35% to 52%.
Grades four to six and nine were this year tested either on a home language level or a first additional language level and all results improved.
The percentage of grade three pupils who obtained at least 50% in maths increased from 17% last year to 36% this year.
This figure decreased from 12% to 11% for grade sixes.
The percentage of grade three pupils who obtained at least 50% in language marks increased from 31% to 57%.
Motshekga said this was "extremely encouraging and should give South Africans great hope that at this rate, we will reach, or even surpass, the targets we have set for ourselves".
Among the grade sixes the language mark increased from 15% to 24% in the first additional language tests and 39% in the home language tests.
The report explained that the assessments were "a critical measure for monitoring progress in achieving set targets in terms of learner achievement".