The Egyptian military in July removed Mohamed Morsi from power. He was elected president the previous year and was a candidate from the Freedom and Justice Party, the Muslim Brotherhood's political arm.
Human Right Watch said it was concerned by a court decision to sentence more than a dozen female Brotherhood supporters to prison on charges of rioting, thuggery and vandalism.
Sarah Leah Whitson, director of the Middle East program at Human Rights Watch, said sentencing pro-Morsi demonstrators to prison is sending a strong message to the Muslim Brotherhood.
"Prosecuting these young women for participating in a demonstration, while security forces who killed hundreds of protesters roam free, should shock our collective conscience," she said in a statement Sunday from New York.
Last week, the rights group accused the military in Egypt of holding officials from the Morsi administration in secret prisons.
The military intervened when protesters expressed frustration with Morsi's pro-Muslim policies. The military-led government has since been accused of using a heavy hand to silence critics wary of its grip on power.
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