Chief Justice Tassaduq Hussain Jilani had taken suo moto action against discrimination of minorities and increasing intolerance towards them.
The court in detailed judgment ordered several steps for protection of non-Muslims and alleviating their grievances.
"A Special Police Force shall be established with professional training to protect the places of worship of minorities," said the judgment.
It also asked the federal government to constitute a taskforce tasked with developing a strategy of religious tolerance, like preparation of appropriate curricula at school and college levels to promote a culture of religious and social tolerance.
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The court ordered that a National Council for minorities' rights should be set up to monitor the practical realisation of the rights and safeguards provided to the minorities under the Constitution and law.
The Council should also be mandated to frame policy recommendations for safeguarding and protecting minorities' rights by the provincial and federal government.
The court expressed satisfaction that registration of marriages of Hindu couples had already started.
It also viewed with satisfaction the steps taken by the government to provide security to the Kalash people in north of the country who were threatened by the Taliban to convert to Islam.