Peshawar High Court (PHC) Chief Justice Waqar Ahmad Seth inaugurated the facility on March 15.
Law and order duties had previously been the responsibility of the Levies Force and Khasadar Force.
If passed, the law would establish a commission to register charities and oversee the collection of donations.
The high court cited the constitutional prohibition on political activity by the armed forces.
Chief Justice Asif Saeed Khan Khosa dismissed the petition 'based on merit' and expressed frustration at the reaction from the extremist minority.
The new measure will help Pakistan meet requirements set by the Financial Action Task Force (FATF) in order to curb the illicit flow of money to terrorists and criminals.
Asif Saeed Khan Khosa, the newly-minted Chief Justice of the Supreme Court, said 'I will do right to all manner of people, according to law, without fear or favour'.
The body is denouncing clerics who pronounce fatwas that favour suicide attacks or falsely label individuals as non-Muslims.
Pakistan officials are investigating whether the Iranian suspects were linked with Iranian intelligence, an official from the Federal Investigation Agency said.
The Sindh Police has set up a dedicated force to control the threat of targeted killings of law enforcement officials and of political and religious figures in Karachi.