A lorry is believed to have dumped the waste in southern Johor state last week, sending toxic fumes across a wide area and causing those affected to display symptoms of poisoning such as nausea and vomiting.
He then decided to order the immediate closure of 34 schools.
"Unfortunately, the situation has become more critical," he said in a statement.
"The education ministry views this seriously as it involves the lives of students and teachers and school workers."
A man suspected to have been involved in dumping the waste will be charged in court as soon as Thursday, the environment minister said.
He faces up to five years in jail if found guilty of breaking environmental protection laws.
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