Scores of girls' schools over recent years have seen mysterious mass faintings, nausea and similar symptoms that are often blamed by police and the local media on poisoning by Taliban insurgents or toxic gas leaks.
But no laboratory evidence of poison or other toxins has ever been found at schools and no deaths have occurred, with the girls often released from hospital after only a few hours.
In the latest case, 200 girls were reported to have been "poisoned" at a school in Kabul on May 1, causing an outbreak of screaming, stomach aches and vomiting.
"I will punish the teacher, I will punish the head teacher and I will punish the school director," he added.
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The education department said the government was determined to crack down on the causes of outbreaks of psychological illnesses among young girls.
"When one student faints, it spreads around and everyone might think it's poisoning," Mohammad Kabir Haqmal, spokesman for the ministry, told AFP.
"If tests prove it is mass hysteria or any other natural cause, of course no one will be punished. What the minister said was that we will pursue those who disrupt the classes."
"The minister should not have said that he will punish schoolgirls," she told AFP. "His job is to find out what has happened and protect schools."
Girls were banned from going to school under the Taliban, but numbers have risen since the extremist regime was ousted in 2001 and the government says 40 per cent of pupils are now female.