Mhlanga said most of the 18 000 books alleged to be short were the textbooks the schools were supposed to get back from pupils at the end of the year.
"Thousands" of undelivered textbooks were found by the Democratic Alliance (DA) during a routine oversight visit to a teachers' training college in Fetakgomo, Limpopo, on Thursday, the party claimed.
DA spokesperson on education in the province Desiree van der Walt said in a statement that security guards prevented the party's delegation from completing its oversight visit, but photographs of the books were taken.
"This is shocking given that schools have had to drag the Limpopo education department to court to get books delivered," she said.
"We have identified at least 47 schools without all the textbooks they need. And now we are discovering warehouses still filled with undelivered textbooks."
Basic education department spokesperson Elijah Mhlanga said the matter was being investigated and he would comment further when the facts were established.
Failure to verify
On Monday he dismissed allegations that some schools in Limpopo had not received textbooks.
More than 6.5-million textbooks had been delivered in 2014 and an additional 306 000 had been ordered to address shortages.
"We acknowledge that there are schools that have reported shortages in February and orders have been made and delivered."
Mhlanga said most of the 18 000 books alleged to be short were the textbooks the schools were supposed to get back from pupils at the end of the year.
Mhlanga said most of the schools involved had failed to check or verify the deliveries of textbooks against the orders placed.
"They only did so after the advent of the 2014 school year."
He said the department had taken steps to ensure that books were delivered on time and that any reported shortages were addressed. – Sapa