Iftikhar Mohammad Chaudhry said, "Military courts are illegal and unconstitutional. The basic structure of the constitution guarantees an independent judiciary, and military courts cannot be established in the presence of an independent judiciary".
The former chief justice, reinstated in 2008 after then military ruler General Pervez Musharraf had deposed him, had taken up cases of missing persons involving the ISI.
He was labelled as an 'anti-military judge'.
The Supreme Court had declared the setting up of military courts as unconstitutional and illegal in 1999.
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After the Pakistani Taliban's deadly attack on an army school in Peshawar that killed 150 people, including 134 children, on December 16, Prime Minister Nawaz Sharif had agreed to a proposal to set up military courts to try terror suspects.
Sharif has announced amending the Constitution to provide constitutional cover to the proposed special courts. He had also lifted a moratorium on the death penalty after six years.
So far six convicted terrorists have been executed during the last two weeks.