The military tribunals were established after the massacre in December, 2014, by militants of 134 students at Army Public School in Peshawar.
Lawmakers authorised the courts in January last year, handing over significant judicial control to a military that is already powerful and has ruled the country of 190 million people for about half of its existence.
They have so far convicted 81 people, 77 of whom were sentenced to death, according to Inter-Services Public Relations (ISPR). There have been no acquittals, the military says.
At least 27 convicts have filed appeals with civilian courts, alleging coercion of confessions and denial of access to lawyers and to evidence used against them, according to Reuters research and local media reports.
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Of the 12 cases that have come before the Supreme Court, the legal arguments have concluded in nine. The court has been hearing the case for the remaining appellants, and is expected to give a verdict on all 12 cases together, possibly in the coming weeks.
Lawyers and relatives of 10 convicts contacted by Reuters have all complained of abuse by the military courts while in custody and of serious procedural shortcomings.
Of those 10, three are before the Supreme Court, one is at Islamabad High Court and six at Lahore High Court.
Reuters was unable to independently verify any of the accusations.
Reuters provided written details of the specific allegations in all 10 cases to the military's public relations wing. The office declined to respond.
Disappeared
One of the convicts, Sabir Shah, was already on trial for murder in a civilian court when he disappeared from Lahore's central jail in April 2015, according to his family and lawyers.
Five months later, his family read a press release saying he had been sentenced to death by a military court.
His lawyers say they still do not know what evidence was used against him. Shah was originally on trial for murder as an alleged member of a sectarian group's hit squad, and that process had not been concluded.
Even after the family filed an appeal with the Lahore High Court, Shah's lawyers said they were not allowed to view the military's evidence.
"All of these things will only become clear to us when we are provided the (military) judgment," said Malik Adeel, who has filed an appeal with the Lahore High Court.
The military said in a press release that Shah confessed to having been involved in the murder of Lahore lawyer Syed Arshad Ali.
Parliamentarians have explained that the courts were borne out of necessity in the face of the militant threat, because the country's judicial system was inefficient and some judges were afraid to take on cases for fear of retaliation.
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"It was endorsed by the parliament. If the normal courts could do the job, why would the military want to do it?" said a senior security official, who asked not to be named because he was not authorised to speak to the media.
At a recent Supreme Court hearing challenging the military tribunals, the Chief Justice questioned whether convicts should be allowed basic legal rights.
"Terrorists are challenging the constitution and the law of the land, but their counsel are citing fundamental rights in their defense," said Anwar Zaheer Jamali, adding that international war crimes precedent allows summary trials and executions.
At a separate hearing, he added: "There are exceptional circumstances, therefore exceptional measures have to be taken by the state for proper dispensation of justice."
The senior security source added: "If someone kills 30 people, you are telling me I should give him justice? Justice should be given to those 30 people killed."
"Coerced" confessions, threats
All the lawyers representing the 10 convicts whose cases Reuters examined said they were denied access to court records and were not allowed to meet their clients for the duration of the military trial.
They also said their clients were either coerced into confessing or deny confessing at all. According to the military's press wing, 78 of 81 accused were convicted on the basis of confessions.
Human rights lawyer Asma Jehangir, counsel for two people who have appealed their death sentences, said her clients were forced to affix a thumbprint to a blank sheet of paper, which was later turned into a confession.
The military declined to comment on those allegations.
Two families and one lawyer also said they had been harassed or threatened after filing appeals.
The father of one convict told Reuters that four family members were abducted by men in military uniform and beaten.
"They said that we have dishonored them and the army as an institution, and that it would be better for us if we withdraw the [appeal]," said the father, who spoke on condition of anonymity for fear of reprisals.
Reuters could not independently verify his account, and the military declined to comment.
Who deserves justice?
The International Commission of Jurists, a non-governmental organisation that promotes human rights through the rule of law, has criticised the army-run courts.
Country passing through abnormal times, says CJP
"Proceedings before military courts fall well short of national and international standards requiring fair trials before independent and impartial courts," it said in a statement earlier this year.
In a televised interview, the army's spokesperson defended the courts.
"Through a due process of law the whole case proceeds, after which the court makes a decision. And then the death sentence or whatever sentence is confirmed," General Asim Bajwa said.
Since 2007, more than 25,000 people have been killed by extremists, according to the South Asia Terrorism Portal.
Pakistan has for years been battling the Tehreek-e-Taliban Pakistan (TTP) and other militants fighting to overthrow the government and impose a strict interpretation of Islamic law.
The number of militant attacks has come down since Pakistan announced an anti-militancy plan after the assault on the Army Public School in December, 2014.
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