The action defied warnings by Turkey, the Greeks' ancient enemy and which occupies the northern sector of Cyprus.
At the same time, Turkey, driving to become the region's paramount power, appeared set for a maritime confrontation with Israel over plans to develop its rich offshore gas fields and link them with those the Greek Cypriots are expected to find.
The plan is to combine efforts to export gas from the Israeli and Cypriot fields, which lie on the same geological belt traversing the eastern Mediterranean from Syria southward to Egypt, via an underwater pipeline to energy-hungry Europe.
Cypriot Energy Service Director Solon Kassinis announced Monday that the Houston company Noble Energy, which discovered the Israeli gas fields in 2009-10, had started drilling beneath the seabed 115 miles of the island's southern coast.
These lie within Cyprus' exclusive economic zone delineated in agreements with Egypt, Israel and Lebanon aimed at facilitating the quest for oil and gas and other mineral deposits.
Turkish Prime Minister Recep Tayyip Erdogan had warned he would send in the Turkish navy to prevent Greek Cypriot drilling and to block Israel from unilaterally exploiting its offshore gas and oil reserves that are due to come on stream in 2013.
In 2010, the U.S. Geological Survey gave some indication of the stakes in the swelling disputes over the region's potential energy wealth. It reported that the continental shelf in the eastern Mediterranean contains an estimated 122 trillion cubic feet of gas as well as at least 4 billion barrels of oil.
The problem is that this intersects with two of the region's long-running disputes, the Arab-Israeli conflict and the traditional rivalry between Greece and Turkey.
Lebanon, technically at war with Israel, is challenging the Jewish state over ownership of some of the gas reserves it has claimed. Both sides have threatened military action.
Turkey, once one of Israel's strongest allies, has fallen out with the Jewish state over the last three years over its occupation of Palestinian land. The dispute climaxed May 31, 2010, when the Israeli navy intercepted a Turkish-led aid convoy headed for the Gaza Strip and killed nine Turks.
Greece's differences with Turkey were enflamed in 1974 when the Turks invaded Cyprus, spurred by a short-lived coup by supporters of union with Greece.
Turkey seized the northern third of the island, proclaimed the Turkish Republic of Northern Cyprus and garrisoned it with 30,000 troops. Only Ankara recognizes the breakaway republic.
The Greek Cypriot government in the south is internationally recognized and, like Greece, is a member of the European Union.
The Greek Cypriots say the TRNC can share in the island's energy wealth once Turkey signs a peace agreement for a federal Cyprus.
Ankara's response has been to initiate its own exploration program, protected by Turkish warships. That will almost certainly trigger a fresh dispute over maritime boundaries.
The two countries came close to conflict in March 1987 when a Turkish research vessel sailed into the Aegean Sea.
Last Thursday, tensions heightened when Athens protested Ankara's dispatch of a Norwegian research ship to search for oil and gas off the island of Kastelorizo.
Greece has already claimed rights to any mineral or fossil fuel deposits around the island as part of its continental shelf.
"Greece may be …far too distracted with its financial crisis to react decisively to Turkey's actions Cyprus," observed the U.S. security think tank Stratfor.
"But if Turkey actually tries to follow through with its threat -- carrying out overflights and providing naval escorts to energy exploration crews in disputed Cypriot waters -- things could get messy.
"And if a hard-pressed Greek government is looking for a distraction to rally public support, a conflict with Turkey may not be a bad idea -- especially if it's one the Turks weren't expecting."
Turkey's threats also pose a challenge to the United States, observed Simon Henderson of the Washington Institute for Near East Policy.
"Washington has a strong interest in eastern Mediterranean countries finding and exploiting offshore reserves," he noted.
"Ankara cannot be permitted to enjoy the benefits of a strong relationship with Washington while undermining U.S. objectives in the eastern Mediterranean."