The ordinance, issued by President Mamnoon Hussain, amended the Pakistan Army Act 2015 to protect the presiding officers of courts, military prosecutors, lawyers and witnesses.
"On a summary initiated by the Ministry of Defence, the president has approved the prime minister's advice and signed/promulgated the Pakistan Army Act (Amendment) Ordinance, 2015," the President's office said in a statement.
The amendment envisages in-camera trial of terrorists and a provision for proceedings through video link.
Dawn reported quoting the Prime Minister's Special Assistant Barrister Zafarullah that the summary was moved by the defence ministry and endorsed by the government.
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He said the amendment was aimed at ensuring security of the presiding officers (judges), lawyers, military prosecutors and witnesses who always remained under threat and were vulnerable to deadly attacks by terrorists for trying their accomplices.
Zafarullah said the government had also tried to protect judges, lawyers and witnesses by putting some relevant clauses in the already enacted Protection of Pakistan Ordinance-2014 (PPO).
"It is not a unique phenomenon - trials of terrorism related cases are commonly conducted through video link in many parts of the world," he said.
It is believed that judges, lawyers, witnesses and prosecution officers remained vulnerable to attacks for trying terrorists, forcing the government to set up military courts for a period of two years.
The bill to set up military courts in Pakistan to fast-track terror-related cases came into effect last month, weeks after the Peshawar school massacre by the Taliban that killed 153 people, including 134 children.