Avigdor Lieberman said each country must respect the sovereign rights of their neighbour, adding that it was "extremely unnecessary" for Turkey to cause friction in a region already mired in conflict.
"We respect the integrity of Cyprus. We're sure that you have your exclusive rights to explore in your economic zone of the gas and oil reserves," he told reporters after talks with his Cypriot counterpart Ioannis Kasoulides.
With Israel finding large reserves of gas close to where Cyprus is drilling, the two countries are looking to cooperate on energy issues such as exporting Israeli gas.
Since October 20, a Turkish survey vessel has encroached Cyprus's exclusive economic zone off the island's southern coast, according to Nicosia.
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.
Cyprus is unhappy that Turkey is determined to search for oil and gas in the same region where Nicosia 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.
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Ankara opposes the Cypriot government's exploitation of offshore energy reserves before a deal is reached to solve the decades-long division of the east Mediterranean island.
Last month Cyprus suspended its participation in UN-led peace talks launched in February.
Despite the United Nations calling on both sides to return to the negotiating table, Greek Cypriot leader Nicos Anastasiades said he will not resume peace talks under "Turkish blackmail".
Ankara opposes Nicosia's exploitation of offshore hydrocarbon reserves before any peace deal, but is itself determined to search for oil and gas in an area the Cypriot government has licensed exploratory drills.
The Greek Cypriots argue that the failure to reach a settlement should not mean such projects are put on hold.
ENI-Kogas began deep sea drilling off Cyprus for possible gas in September in a second block to undergo exploratory tests since the first find in 2011.
US firm Noble Energy made the first find in the Aphrodite field, which is estimated to contain 102 billion to 170 billion cubic metres (3.6 trillion to six trillion cubic feet) of gas.