Islamabad High Court (IHC) Justice Shaukat Aziz Siddiqui on Wednesday criticised the alleged interference of the country's intelligence agencies in the affairs of the judiciary, media and the executive, warning that such an intrusion may eventually lead to a "big loss".

Justice Siddiqui, who is the senior puisne judge of the IHC, made the observations while wrapping up a case concerning two missing brothers who were allegedly disappeared by a spy agency.

The judge is currently facing a trial in a reference on misconduct moved in the Supreme Judicial Council on the complaint by a retired employee of the Capital Development Authority for alleged refurbishment of official residence beyond entitlement.

Justice Siddiqui also made headlines last year when he criticised the armed forces for their role as the "mediator" in the agreement that led to an end of the sit-in by religious groups at Islamabad's Faizabad Interchange in November.

"Who is the army to adopt a mediator's role?" the judge had questioned at the time. "Where does the law assign this role to a major general?"

In the order sheet issued after today's hearing, Justice Siddiqui not only censured Islamabad police for their failure to protect citizens from enforced disappearances, but also criticised intelligence agencies, especially Inter-Services Intelligence, for allegedly exceeding their sanctioned mandate.

The judge observed that “police is in league with the mighty agencies, who have disrupted the civic fiber of the country by establishing [a] state over the State of Pakistan”, and warned that this is leading to what he termed a “disastrous situation”.

“I must observe that persons [at] the helm of affairs of all the institutions need to protect [their] hard-earned independence and take remedial steps to stop the invasion by [the] personnel of [a] particular institution and intelligence agencies,” the court order noted.

Read the complete IHC order

Accusing the spy agencies of interfering in the affairs of the third pillar of the state, Justice Siddiqui wrote: “Everyone knows [...] how proceedings are manipulated, from where strings are pulled and when power [is] wielded and maneuver[ed] to achieve the desired results.”

“It is [a] matter of great concern that even benches are constituted and cases are marked to different benches on the direction of such elements,” he added.

Justice Siddiqui's remarks came after he, despite being a senior puisne judge, was not included in a division bench formed to hear appeals filed by ex-prime minister Nawaz Sharif, Maryam Nawaz and retired Captain Mohammad Safdar against their conviction in the Avenfield properties reference.

Instead, the division bench was formed comprising two junior judges. The bench has since taken up the appeals and adjourned proceedings till after the July 25 general elections.

The order sheet today read, “It is time to save the institution of the judiciary from all kind of influences, otherwise we may not be able to answer [to] Allah Almighty.”

“To remain like a silent spectator is against the oath made by every judge, provided by the Constitution. In case of our failure, the Pakistani nation and history will not remember the judges with good names [sic],” it added.

Justice Siddiqui directed court officials to forward a copy of the order to the defence and interior secretaries as well as to the chief of army staff and the ISI director general.

Earlier, Islamabad police had produced Rabnawaz, a man who was allegedly picked up by unknown persons, before Justice Siddiqui.

The abductee had told the court that “he went to Vehari on his own.” However, his brother, Iftikhar Raja, had stated that Rabnawaz was perjuring himself and that he had in fact been abducted by spy agencies and subjected to physical and mental torture.

Raja said it was in his knowledge that his brother had been harassed and threatened with dire consequences in order to prevent him from recording any statement contrary to what has been dictated by his abductors.

In the order sheet, Justice Siddiqui noted that “it is expected from the top echelon of [the] army that by appreciating the delicacy, sensitivity and alarming [nature of the] situation, some remedial steps to stop their agencies from interfering into the affairs of other departments and to refrain [them] from assuming the role not assigned by [the] law shall be taken."

If the measures are not taken, the judge concluded, "these practices shall ruffle the people of Pakistan, which by no stretch of imagination is good for the prestigious institution of the Pakistan Army as well as the Islamic Republic of Pakistan."