Defence Minister Chistoforos Fokaides said the vessel was being closely monitored and that Nicosia would examine "its response to defend its rights and sovereignty".
Nicosia is unhappy that Ankara is determined to search for oil and gas in the same region where the Cypriot government has already licensed exploratory drills in an exclusive economic zone.
Turkish troops invaded and occupied the northern third of Cyprus in 1974 in response to an Athens-engineered coup aimed at uniting it with Greece.
Earlier this month Cyprus suspended its participation in UN-led peace talks launched in February, during which Greek Cypriot leader Nicos Anastasiades was to meet Turkish Cypriot counterpart Dervis Eroglu.
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Anastasiades today chaired an emergency meeting of political leaders to discuss how Cyprus should respond to the Turkish action.
Satellite maps of marine traffic in the region show that a Turkish vessel, the Barbaros, had moved to around 20 nautical miles off the island's southeastern coast at Cape Greco near the exclusive economic zone.
The movement of the Barbaros and accompanying ships -- two support vessels and a Turkish navy frigate as shown by the maps -- are "provocative and illegal," Fokaides told state radio.
Nicosia is "now obliged to escalate its response to defend it rights and sovereignty", he said.
"We have already studied alternative scenarios. This move by Turkey was one of the scenarios that we studied, we are not surprised that it carried through on its threat," Fokaides said.
Ankara had issued a notice that a Turkish seismic vessel would carry out a survey from mid-October to December 30 in the same area where the Italian-Korean energy consortium ENI-Kogas is operating.