The Home department of the government of the Punjab province instructed churches in the region via a letter that missing the deadline would result in closures until the government's safety standards are met.
Several churches have been attacked in the past, with hundreds of people being killed in these attacks as well.
However, Centre for Legal Aid Assistance and Settlement (CLAAS) - the Christian charity dedicated to helping persecuted Christians in Pakistan, said the measure was unfair.
It a statement, CLAAS said: "But the government has failed to bring the perpetrators to justice and now instead of providing security to them, it is shifting its responsibility to the churches.
"The majority of churches are poor, and it will not be possible for many of them to make their own security arrangements, sadly resulting in some churches facing closure."
The government has not issued guidelines on what the minimum security standards for churches are.
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