Human Rights Watch said there were a large number of civilians on trial in military courts for what it said were nothing more than "major" attacks on free expression.
Human Rights Watch said military authorities prosecuted youth leader Asamaa Mahfouz for insulting the military.
"The military is using her to silence potential critics, sending the message that criticizing the current military government will land them in jail," Joe Stork, deputy Middle East director at Human Rights Watch, said in a statement.
Human Rights Watch said military authorities last week questioned Mahfouz about statements posted on her Twitter account in July complaining the military wasn't doing enough to protect civilians.
As many as 43 cases similar to Mahfouz's are ongoing in military courts, the rights group said.
At least 10,000 civilians were sentenced this year in what Human Rights Watch said were unfair proceedings. All of them should be retried, the group added.
"Egypt needs to urgently review the legal framework which (deposed President Hosni) Mubarak used for years to silence his critics," concluded Stork.