Egyptian Interior Ministry spokesman Abdel Fattah Othman told the Egyptian Independent news agency that two people died and another 89 were injured following clashes outside the Coptic Orthodox Cathedral in Cairo.
Visiting Ashton said she was alarmed by the violence, but had assurances from Egyptian President Mohamed Morsi that the situation was under control.
"I am extremely worried about the violent incidents at the Abaseya Coptic Cathedral in Cairo," she said in a statement. "On hearing the news I immediately contacted the Presidency, strongly urging restraint and for the security forces to control the situation."
Morsi's administration has been criticized for appearing to embrace policies that favor conservative Islamic ideologies. He hails from the Muslim Brotherhood's political arm. There were no indications that those policies were to blame for the latest violence, however.
Morsi changed recent election dates to accommodate Easter celebrations in late April under the Coptic Christian calendar.
The Interior Ministry spokesman said the situation was under control by Monday. At least 16 police officers were among those injured.
Nearly two dozen members of the Coptic community were killed in an attack on a church in Alexandria in January 2011.