The bills were presented to the parliament after political parties and army agreed in a marathon meeting yesterday on the mode of setting up the courts.
The 21st Constitutional Amendment Bill and Pakistan Army (Amendment) Bill 2015 were presented in the National Assembly by Minister for Law, Justice and Human Rights Pervaiz Rashid.
Prime Minister Nawaz Sharif was also in the house when the bills were presented.
The bills have to be passed by at least two-third majority in both the 342-seat National Assembly and the 104-seat Senate before they go to the president and become part of the constitution.
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The amendment will provide constitutional cover to the establishment of military courts in the country.
The law aims to give a tough message to militants who often wriggled out of ordinary courts.
It is being enacted as part of several measures to eliminate militancy. Pakistan has already lifted moratorium on death penalty and hanged seven convicted militants.