Officials said it would affect only those accused of acts of terrorism.
But Amnesty International warned that the measure was so vaguely worded that it could be used to try government critics, including peaceful activists.
Civilians last faced military trials during a three-month state of emergency declared in 2011 after the authorities suppressed mass pro-democracy protests.
About 300 people were convicted of political crimes during that period, after what Amnesty International said were grossly unfair tribunals characterised by a range of violations, including the admission of "confessions" obtained under torture.
The previous constitution said the jurisdiction of military courts was "confined to military offences committed by members of the Bahrain Defense Force, the National Guard and the Security Forces" unless martial law was declared.As reported by the BBC.