An editorial "Unbridled military courts" in The Nation said that the Supreme Court may have given the military courts its seal of approval, "but it did not do so without any provisos".
"Eight out of 13 judges held that trials by the courts were subject to certain safeguards to insure that a fair and diligent trial takes place. Yet, the same government which heavily cited the judgement to claim that the courts were justified, is now ignoring the recommendations made by the apex court to establish these safeguards," said the daily.
It added that if the government considered the judgement valid "then it must agree to the entirety of it, not cherry pick the clauses favourable to it".
On Wednesday, the Senate passed the Pakistan Army (Amendment) Bill 2015 without including any of the safeguards recommended by the Supreme Court. Having been passed by both houses, only the presidential signature is needed for it to become law.
"...This bullish haste is inexplicable, as the recommendations of the Supreme Court are not demanding nor do they interfere with the functioning of the military courts in any way," said the daily.
The editorial said that the recommendations include a reference to military courts by the federal government was subject to judicial review, the military courts were bound to provide the accused with fair trial and reasonable procedural safeguards and the judgments of the military courts were subject to judicial review by the superior courts.
"All of them reasonable and non-intrusive. The first insures that only terrorists are referenced to the military courts, not political prisoners, and the second is a no-brainer, which no government in the world should disagree with, and the third insures the military courts follow the law."
The daily said that had the government listened to the Supreme Court, "the military courts could have become a relatively acceptable and uncontroversial institution".
"In their present state, they are highly secretive, supremely powerful, and completely unaccountable."