Extending the protocol is a key condition before Turkey can begin EU accession talks in Octoberm but Ankara says the protocol will not amount to recognition of the Greek Cypriot government.
Cyprus has threatened to veto the start of Turkey's EU talks if it is dissatisfied with Ankara's stance and says the protocol means Ankara must let Cypriot planes enter its airspace and Cypriot-flagged ships call at Turkish ports.
In Brussels, a commission spokeswoman confirmed on Tuesday that the EU executive had received Turkey's letter and would set in motion a decision by EU ministers leading to the signature of the accord in time for Turkey to start EU entry talks on 3 October.
The Turkish move, equivalent to initialling the protocol, "certainly creates a better atmosphere in the preparations for starting talks", commission spokeswoman Krisztina Nagy said.
''The signing of the protocol is not a legal and formal recognition of the Republic of Cypru."
Gul (R) said the signing is unlikely
to take place before July
Cyprus joined the EU last May represented by the Greek Cypriot government. Ankara backs a tiny Turkish Cypriot enclave in the north.
"We have begun the process of signing the protocol. Today the commissioner for enlargement will give information on this issue, probably at the European Parliament. But we have given our approval," Turkish Foreign Minister Abdullah Gul said.
Gul, in a televised speech to his ruling Justice and Development Party (AKP), said the protocol covered only the free movement of goods and did not require Turkey to open its ports and airports to the Cypriots.
Nagy said the commission considered the Turkish restrictions on vessels and aircraft from Cyprus violated the customs union.
"The commission has consistently reminded Turkey that those restrictions have to be removed, most recently at the last (EU)Troika meeting in Ankara (on 7 March)," she said. "Under the customs union, such restrictions cannot exist."
"Under the customs union, such restrictions cannot exist"
European Union spokesperson
A Cypriot shipping industry representative said Turkey must lift its ban on Cypriot-flagged ships.
Turkey banned Cypriot ships from its ports in 1987, but the industry says the blockade had really begun to pinch since 1998, when new international shipping regulations were introduced obliging owners to clearly identify themselves.
"Turkey cannot begin talks with the EU unless this trade embargo is lifted," Thomas Kazakos of the Cyprus Shipping Council (CSC), which represents shipowners and managers throughout Europe, told Reuters on Tuesday.
He blamed the ban on a decline in the number of ships registered in Cyprus, which just three years ago had the world's fourth largest fleet.
The fleet is now the world's eighth largest and the EU's third largest. The protocol must be ratified by the Turkish and European parliaments. But signature, not ratification, was the condition for starting the accession talks, Nagy said.
Gul said the signing was unlikely to happen before July.