"It was a difficult year in many respects, not only in terms of Limpopo, which received lots of attention but also the Northern Cape and the Eastern Cape," she said.
"All the efforts we made do not mitigate against the difficulties."
By June this year thousands of teaching posts in the Eastern Cape were left vacant and in August the Grahamstown High Court ordered the provincial education department to fill the positions.
In the Northern Cape's John Taolo Gaetsewe district 16 000 students were forced to stay away from school for four months by a community protesting poor service delivery.
The textbook delivery crisis in Limpopo was not an issue that affected matrics though, she said, as these were restricted to grades one, two, three and 10.
Motshekga said she was confident schools and provinces had done all they could to protect children and that, despite the difficulties, they were prepared to go through with the exams.
"We did everything we could to support learners in every way we could," she said.
Motshekga said it was "all systems go" for the 2012 National Senior Certificate (NSC) exams, which begin next Monday and continue until late November.
Motshekga was speaking at a press briefing in Pretoria to discuss the department's readiness to administer matric exams. There are 527 335 full-time and 120 352 part-time candidates enrolled to write the NSC exams this year.
The low number of candidates writing pure maths and the drop in the number of students taking physical science as a matric subject was "an area of great concern" and an "ongoing problem" for the department, she said.
The number of students writing maths has increased slightly – from 229 371 last year to 230 194 this year, while the number of students writing physical science has dropped from 184 052 to 182 083.
Despite the increase on last year's number, the number of students writing maths is still 27% lower than it was in 2008 and there has been a 20% decline in the number of students writing physics in the past five years.
Motshekga said there were a number of factors behind the decline in interest in maths and physics.
"It's [driven by] schools themselves, in a drive for higher pass rates, but also parents and learners themselves. Not wanting to risk failure, they go for maths literacy rather than pure maths," she said.
Motshekga said the department was awaiting a report on the issue and planned to call a maths and science summit later this year, to investigate strategies to strengthen performance in the subjects.
Motshekga said the department was ready to deliver "credible and fair examinations" and did not foresee any major discrepancies or irregularities. She said despite initial "teething problems" with the National Curriculum Statements, the system had stabilised.
"Over the past two years we have not experienced any question paper leaks, nor any serious incidents that could compromise the credibility of the NSC examinations," she said.
She outlined a number of strategies implemented to improve the quality and credibility of the system, including increases to the number of examiners and moderators and the development of a common language assessment framework to ensure there is comparability between the standards of all language question papers.
This year the department is also piloting competency tests for markers in seven subjects. Paddy Padayachee, deputy director general in the department, said the idea was to eventually institute competency tests for markers in all subjects.
The department has published a gazette announcing its intention to institute the competency tests and is awaiting stakeholder input before the system is fully implemented.
Motshekga said the question papers for the exams have been secured in safe rooms at undisclosed locations to ensure their safety. "The security of question papers and scripts before and after examinations cannot be overemphasised," she said.