"The EU urges Turkey to refrain from any kinds of threats, sources of friction that could negatively affect good neighborly relations and the peaceful settlement of border disputes," a spokeswoman for the EU's foreign policy chief Catherine Ashton told reporters.
Maja Kocijancic said Turkey should work towards a "comprehensive" solution to a conflict between Turkey and EU member Cyprus over the northern part of the Mediterranean island.
Erdoğan issued the veiled criticism of Cyprus during a television interview on Thursday, in which he said Ankara would send warships to escort aid vessels to Gaza in a step up of confrontation between Turkey and Israel.
He said Turkey, a NATO member, has taken steps to patrol the Mediterranean, and vowed to stop the Jewish state from exploiting natural resources in the area.
"You know that Israel has begun to declare that it has the right to act in exclusive economic areas in the Mediterranean," Erdoğan said, apparently in reference to Israeli plans to exploit offshore gas reserves found in areas that are also claimed by Lebanon.
"You will see that it will not be the owner of this right, because Turkey, as a guarantor of the Turkish republic of north Cyprus, has taken steps in the area, and it will be decisive and holding fast to the right to monitor international waters in the east Mediterranean," he said.
Turkey argues the oil deals are illegal as the borders of Cyprus remain undetermined while Greek Cypriots and Turkish Cypriots pursue reunification talks.