An additional 21 male supporters were referred to the military court in the same case.
The 30 defendants were accused of participating in unlicensed protests and having links with a "terrorist" movement, namely Morsi's Muslim Brotherhood group.
The date of the military trial for the 30 defendants has yet to be set.
Four of the nine female defendants were arrested on December 27 of last year; four on March 30 of this year; and one in February of this year.
They were all accused of violating Egypt's protest law by staging protests outside government institutions, blocking roads and affiliation with a "terrorist" group.
It was the first time for female Morsi supporters to be referred to a military court since Morsi's ouster on July 3 of last year, according to a legal source from the National Alliance for the Defense of Legitimacy, Morsi's main support bloc.
"The nine women were referred to court retroactively, which is unusual in legal practice," the source said.
The source added that charges leveled against the nine women dated back to December of last year and March of this year, even though the law under which they have been referred to court was only issued in October of this year.
"This means the trial will be conducted in total contravention of the law," the source said.
In October of this year, Egyptian President Abdel-Fattah al-Sisi issued a law classifying all government institutions and public utilities as "army facilities."
This means that anyone found violating these institutions or utilities would be liable to trial in military court.
Presidential spokesman Alaa Youssef said the law had been issued with the aim of protecting state institutions and securing citizens.