The army said the special military courts have the trial of 12 militants whose cases were referred by the government.
Military spokesman Major General Asim Saleem Bajwa said the military courts were trying cases sent by the Interior Ministry through "already defined criteria."
"Cases to be tried by military courts are forwarded by provincial apex committees to the Interior Ministry which after due scrutiny further sent to army," he said.
Pakistan decided to set up the courts after Taliban gunmen killed nearly 150 people, mostly children, in a brazen assault on an army-run school in Peshawar on December 16.
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The courts were established in line with the 20-point National Action Plan finalised by its political and military leadership to fight militancy.
The courts have been set up for two years and are staffed by serving military officers.
Following the Peshawar attack -- one of the most brutal in its history-- Pakistan also ended a self-imposed moratorium on death penalties in terror cases.
The military claims to have killed more than 1,600 militants in the North Waziristan tribal region so far.
Although human rights groups have severely criticised the setting up the military courts when civilian judicial forums are available, the government and army have said traditional courts take too long to decide such cases.
The authorities also claim that civilian courts and judicial forums are often vulnerable to threats and intimidation by militants.