A three-judge bench headed by Chief Justice Iftikhar Chaudhry issued the notices on Wednesday after admitting a petition filed by a woman whose three sons were picked up by intelligence operatives for their alleged role in attacks on the army's General Headquarters and the ISI's Hamza Camp base in Rawalpindi.
The woman's sons were detained along with eight other men, and four of the suspects have died in mysterious circumstances over the past six months.
The suspects were being tried under the Army Act.
The bench also issued notices to the Attorney General, the Advocate General of Khyber-Pakhtunkhwa, the army's Judge Advocate General and the army commanding officer involved in the detentions.
The bench directed the respondents to file their replies by January 30.
The bench took up the constitutional petition filed by the woman, identified only as Ruhaifa, after removing objections raised by the Supreme Court Registrar's office.
Ruhaifa petitioned the court for the provision of "due process of law" to her sons Syed Abdul Saboor, Syed Abdul Basit and Syed Abdul Majid saying "The matter is of public importance and there is apprehension of deaths of the
After the apex court's Registrar raised objections to the petition, Saboor was killed by intelligence agencies, his brother Mufti Shakoor told The Express Tribune newspaper.
During Wednesday's hearing, the bench observed that media reports suggested that the bodies of the suspects were being left by the roadside for their families to collect.
Ruhaifa's counsel told the judges that three of the detained men died because of torture and slow poisoning, and asked the court to direct authorities to submit comprehensive reports on the circumstances surrounding their deaths.
Ruhaifa's sons published scripture and religious literature in Lahore's Urdu Bazaar.
They went missing in November 2007 after they were taken to a police station.
When Ruhaifa approached the Lahore High Court for the release of her sons, she learnt they had been booked under the Anti-Terrorism Act.
They were acquitted by an anti-terrorism court in Rawalpindi in April 2010. However, before they could be released, the Punjab Home Department extended their detention in May 2010 for 90 days under the Maintenance of Public Order Ordinance.
These detention orders were set aside by the Lahore High Court the same month.
On May 29, 2010, authorities at the Rawalpindi jail handed over Ruhaifa's sons and eight others to intelligence agencies instead of releasing them.
When the matter came up for hearing in the Supreme Court, the heads of the ISI and MI conceded that the men were in the custody of their agencies.
The Advocate General too acknowledged that the men were formally arrested in the first week of April 2011 and a case had been registered against them under the Pakistan Army Act.
Ruhaifa has asked the apex court to determine whether the deceased and surviving detainees, including her sons, were subject to the Army Act.
She asked the court to declare that the detained men were in illegal confinement and had been tortured.