The Basic Education Department on Wednesday admitted it failed to efficiently deal with so-called "inappropriate schools".
Almost 500 such institutions have been identified nationwide.
Most have been deemed inappropriate for teaching and learning due to infrastructure problems.
Many are located in the Eastern Cape, where there is a considerable backlog in improvements.
Basic Education Deputy Director General Shunhugam Padayachee said, "We are more than disappointed with our performance."
The department has also come under fire for failing to deliver textbooks to Limpopo pupils.
Some learners in the province are yet to receive books.
Meanwhile, Congress of the South African Trade Unions (Cosatu) and several other groups have announced they will be marching to both the Western Cape Legislature and Parliament this weekend.
They are protesting against the proposed closure of 27 schools in the province.
The institutions have been identified for possible decommissions due to either poor performance or dwindling numbers.
Cosatu and lobby group Equal Education say they expect thousands of people to participate in the march.
The federation's Tony Ehrenreich says they plan to fight closures until an agreement is reached.
Equal Education has indicated it is worried about overcrowding at other institutions, should all the closures be implemented.
Public hearings on the issue have been concluded and Education MEC Donald Grant is expected to make a final decision by the end of September or early October.
Up to 4000 pupils may be affected.