An official of a private school in the Azizabad area said on condition of anonymity that deputy commissioners of three districts in Karachi had sent letters to some schools in their respective jurisdiction giving the new instructions.
"They have said that if parents of any students don't allow the school administration and polio vaccine teams to immunise their children, strict action should be taken against them," he said.
The matter has come to an head in some areas of the city after anti-polio vaccine teams were not allowed to enter some private schools in some areas as part of a nationwide immunisation drive last week.
In some cases, the school administration had refused to allow the polio vaccination workers to enter their premises insisting that parents were not comfortable with getting their children immunised in such drives.
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The government has made refusal to allow immunisation against polio a criminal offence since last year when nearly 4000 people in Quetta, Pishin and Killa Abdullah districts in Baluchistan province refused to allow their children to be vaccinated.
Pakistan and neighbouring Afghanistan are the only two countries in the world where polio remains endemic.
Pakistan's polio cases are declining, with just 54 cases of wild polio virus reported last year, down more than 80 per cent from 2014.
Scores of health workers in Pakistan have been killed in the last two years as a result.
Polio workers have long been targeted in the country by Islamist groups including the Taliban militants which claim that the polio immunisation drive is a front for espionage or a conspiracy to sterilise Muslims.