The amendments allow appeals of verdicts in misdemeanour trials and requires the opinion of the Grand Mufti in verdicts of capital punishment, as is the case in civil courts.
In cases of verdicts issued in absentia, military courts adopt the procedures of criminal law in civil courts, Ahram Online reported.
Under the new law, military courts will also be renamed to mirror those of civilian courts, the report said.
Rights groups and activists have criticised the new law.