Turkey dispatched a research vessel to the south of the island late last year while companies commissioned by the internationally recognised government explored offshore.
"My participation in a dialogue for a solution to the Cyprus problem is not possible for as long as the sovereign rights of the Republic of Cyprus are being violated,» Cypriot President Nicos Anastasiades said in a written statement.
Anastasiades, who leads a Greek Cypriot government, pulled out of peace talks in October, viewing the presence of the research ship as a challenge to Cyprus's offshore rights.
Local media reports said the Turkish vessel, which specialises in collecting seismic data, was now docked in Turkish-occupied Cyprus, awaiting fresh instructions from the Turkish government.
Cyprus and its partner, U.S. energy company Noble, made the first offshore natural gas find in late 2011. A consortium of Italy's ENI Spa and South Korea's KoGas is now exploring other areas south of the island.
Turkey says Cyprus has no rights over natural gas and any finds should be equitably shared with Turkish Cypriots. Cyprus says both sides can reap the benefits of gas discoveries once the island is reunited.