The defendants, many of whom are supporters of ousted Egyptian president Mohammed Morsi and members of the Muslim Brotherhood, were sentenced to death for their alleged involvement in an attack on a police station in the town of Kerdasa in August 2013, in which 11 police officers were killed in the incident.
The Foreign Ministry released a statement on Tuesday saying the ruling was "far from a fair trial" and would not provide Egypt with permanent peace or stability.
"We will continue our solidarity with the brotherly Egyptian people," the statement read.
Last December, a court referred the defendants to Egypt's grand mufti, the country's top religious authority, to consider possible death sentences.
The mufti's opinions are not binding on the court, but Egyptian law requires judges to seek a religious point of view before any death sentences are handed down.
The court later commuted the death sentence against one convicted minor to 10 years while acquitting two others. Another two reportedly died in custody.
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