EU foreign policy chief Catherine Ashton on Sunday said the 28-member bloc was following developments in Egypt with "deep concern", deploring recent violence and calling for prompt elections.
Egypt's first freely elected president, Mohamed Morsi, was overthrown in a military coup on July 3 after millions took to the streets calling on him to step down.
Since then, Morsi's Muslim Brotherhood movement has led demonstrations against the ouster, urging an "uprising" after accusing troops and police of "massacring" its supporters during dawn prayers on Monday when 51 people were killed.
Morsi has not been seen in public since he was toppled, but Egypt's interim leaders say he is being held in a "safe place, for his own safety," despite calls by the United States and Germany for his release.
"The EU is following the recent developments in Egypt with deep concern," Ashton said in a statement, adding that "the military must accept and respect the constitutional authority of the civilian power".
She also stressed "the importance of holding democratic elections in the shortest possible time" and called for dialogue between all political groups committed to democracy.
"The EU urges the interim authorities to make every effort so that politically motivated arrests and other forms of harassments do not take place," she said, adding that "all political detainees must be released, and criminal cases reviewed swiftly in a transparent manner."