Police have reportedly asked the provincial education department to close Naphakade school after pupils protesting overcrowding set fire to classrooms on Tuesday and clashed with police.
Some 1 500 primary and secondary pupils are crammed into 25 classrooms at the school.
Motshekga said in a statement that violence was unacceptable.
"By choosing to resort to this kind of illegal action, learners may not only jeopardise their own futures, but have disrupted learning and teaching for the whole school," she said.
"There are far more responsible and effective ways of raising issues around education, without destroying property or disrupting schooling."
Western Cape education MEC Donald Grant said earlier on Wednesday that the violence was "wholly unnecessary", as his department had prioritised the construction of a new school in the area.
Money had already been budgeted for a new high school in the area.
"We are determined to ensure that the new school opens at the beginning of 2012," he said.
"This new school will alleviate overcrowding and will ensure quality learning for all learners," Grant said.
Four students, aged 21, 20, 18 and 16, were charged with public violence and arson. They were due to appear in the Malmesbury Magistrate's Court on Wednesday.