A three-judge bench headed by Chief Justice Iftikhar Chaudhry issued notices to the Law, Information and Interior Secretaries to submit their responses to the petition filed by a journalists' organisation at the next hearing on Monday.
The court also directed the government and the police chiefs of Punjab and Islamabad to submit detailed reports on the investigations conducted so far into Shahzad's killing.
The bench was hearing a Constitutional petition filed by the Pakistan Federal Union of Journalists (PFUJ) seeking the formation of an independent judicial commission headed by an apex court judge to probe the murder.
The PFUJ approached the apex court after a judicial commission formed by the government to probe Shahzad''s death ran into problems within hours of its creation yesterday.
Supreme Court Justice Saqib Nisar, chosen by the government to head the commission, said he could not take up the task as the Chief Justice was not consulted about the appointment.
Nisar said he would have accepted the responsibility if the government had taken the Chief Justice into confidence first.
Supreme Court Bar Association President Asma Jahangir and senior lawyer Munir Malik appeared on behalf of the PFUJ at the hearing.
Outside the court, Jahangir told reporters there were allegations that a "powerful federal agency" was involved in Shahzad's death.
Such powerful institutions needed to be controlled, she said, without naming the federal agency.
Jahangir said she had learnt from a representative of the Punjab government that the investigation into the killing had reached a "dead end".
There were reports that Shahzad's mobile phone records had been partially erased, she indicated.
The PFUJ''s petition also asked the apex court to direct the government and law enforcement agencies to appoint a competent police officer to investigate Shahzad's case and provide complete protection to journalists.
Shahzad went missing in Islamabad while driving from his home to a TV station on May 29, two days after he alleged in an article that the Pakistani navy had been infiltrated by al-Qaeda.
His body, bearing marks of torture, was found in a canal in Punjab province.
Journalists' organisations and rights groups blamed the ISI for Shahzad's death, a charge denied by the powerful spy agency.