The department said the schools where these pupils get placed and their subject advisers would assist with catch-up plans as they would be behind.
Education MEC Debbie Schäfer said this year saw a massive increase of 18 285 pupils compared to last year's 16 285 - mostly from outside the province.
“Realistically, to accommodate this growth, we would need approximately 15 new additional schools and over 480 teachers.
"More than 130 000 learners have moved to the Western Cape from other provinces in the past five years, mainly from the Eastern Cape, placing the education system in the Western Cape under considerable pressure,” she said.
Schäfer said six new schools were built last year, including three new mobile schools, as were 46 additional mobile classrooms and 34 new brick-and-mortar classrooms.
The department ordered an additional 70 mobile classrooms last week.
It had also increased its spend on infrastructure from R445 million in 2009/10 to R1.6 billion in 2018/19.
Disgruntled Mfuleni Learner Representative Council leaders protested on Friday in solidarity with the more than 1 000 of their peers who haven't been allocated places at local schools.
The children, ranging from grades R to 11, have been crammed into halls, old clinic buildings and churches.
They are currently being taught by unemployed teachers who have volunteered their time.
A nearby school has also been assisting with feeding the children.
Department spokesperson Jessica Shelver said primary school pupils would platoon with a nearby school until a new school was built on the Fairdale site.
High school pupils would also platoon with a 16-classroom school in the Silver Sands area.
In a statement, Shelver said: “A (Mfuleni) school requested to close for safety reasons as protesters outside were violent. Another school was stoned.
"It is alleged that some community members, reportedly those who are seeking placement for their children, have now disrupted teaching and learning at all Mfuleni schools, indicating that no learner in Mfuleni will attend school until every child can be accommodated.”
She said they had tried the diplomatic approach with the Mfuleni Forum and would now lodge a complaint with the police.
Community leader and parent Sipho Delana said parents became frustrated when they were informed that their children must stay home.
South African Democratic Teachers Union provincial secretary Jonavon Rustin said: “The department is looking in the wrong place. They need to make assessments on the number of learners in former Model C schools and decide when a school is full.
"We suspect that there are a number of schools in the wealthy suburbs that just refuse to take learners while they can accommodate these learners.
“These schools are not willing to compromise and make space, hence we have these 5700 learners that have not been placed.
"We have schools in the poor areas that are forced to accept many learners regardless of the number that already exist in the small classrooms.”
Rustin said the department needed better planning because it had been known for a number of years that Mfuleni, Lwandle and Mitchells Plain were areas which were growing in population size.
He said the department was contradicting itself in that it wanted to close some schools, yet said it needed 15 more.