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Books for 1.5 million pupils at 5,582 schools in the province were still in a warehouse on Military Road in East London.
Most children who were meant to have been supplied with the books at the beginning of the school year on January 9 received them only a month later, reported the newspaper.
The basic education department said this week that 99% of government schools had received textbooks.
But Eastern Cape education superintendent-general Modidima Mannya said there were still "serious shortages" with the wrong books having been delivered to schools in certain cases.
"I am not going to comment in the event I am accused of attacking somebody," Mannya said.
The department is responsible for printing 54 million books for delivery to 24,355 schools.
Claims of books not reaching their destination emerged after Mannya commissioned a forensic investigation into several hundred schools that failed to pay a total of R7-million to suppliers though they had received funding from the department.
Mannya said it was not the first time books had not been correctly delivered.
Peter Moses, head of department at Breidbach Primary, said he notified the department on February 16 about isiXhosa textbooks and was still waiting for a response.