According to AFP Mogherini said they recognized Turkey faced real security concerns, but echoed U.S. Secretary of State Rex Tillerson's call for Ankara not to go over the top in its response.
After talks in Ankara, Tillerson and his Turkish counterpart Mevlut Cavusoglu said they had agreed to work together in Syria, easing tensions.
Mogherini said EU foreign ministers had raised the offensive with Turkish European affairs minister Omer Celik, who joined them at a meeting in the Bulgarian capital Sofia.
"We have expressed as the European Union and member states in recent days and weeks concern about first of all the civilian casualties, about the humanitarian consequences of this military operation," Mogherini said.
"The target of military operations needs to continue to be Daesh (IS) and the UN-listed terrorist organizations. I would subscribe to the words that Rex Tillerson said, that we urge our Turkish friends to show restraint in their military actions."
Turkey last month launched an operation in northern Syria against Kurdish forces, the Syrian People's Protection Units (YPG), which Ankara blacklists as a terror group, but which is closely allied with the U.S. in the battle against IS.
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