Romano Prodi's diplomatic mission on Thursday prepares the ground for the EU's December decision on whether to open accession talks with the 15-nation bloc.
He is the first president of the EU executive to visit Turkey since Ankara signed an association agreement with the European Economic Community in 1963.
Turkey has been an EU candidate since 1999, but is the only country among 13 states not to have begun accession talks with the pan-European bloc.
EU leaders are to decide in December 2004 whether the strictly secular and western-oriented country has made enough progress in democratic reforms to open membership negotiations.
Ankara argues that it has fulfilled all the political criteria required to open membership talks and earned the right to begin negotiations.
Accompanied by EU Enlargement Commissioner Guenter Verheugen, Prodi made no comments upon arrival and was immediately whisked to a red-carpet reception with Turkish Prime Minister Recep Tayyip Erdogan.
But at a press conference on the eve of his visit, Prodi welcomed "huge progress" by Turkey to enact EU-oriented reforms, but said "we'll also look at the question of implementation of legislation on the ground".
The Union has also told Ankara that it needs to help broker a settlement to the long-standing division of Cyprus if it wants to join the bloc.
An EU summit in Brussels last December underlined "the importance of Turkey's expression of political will to settle the Cyprus problem. In this respect a settlement of the Cyprus problem ... would greatly facilitate Turkey's membership aspirations".
Turkey rejects any link between the Cyprus question and its own EU aspirations, but Foreign Minister Abdullah Gul acknowledged in a newspaper interview on Thursday that failure to resolve the dispute could prove costly.
Turkish Cypriot Rauf Denktash has
rejected UN unification plan
"We are running late for a solution. Our hand is weakening. We cannot get rid of a problem by postponing it. This is where we are at in Cyprus," Gul said in comments published by the liberal Radikal daily.
Cyprus has been divided along ethnic lines since 1974 when Turkey occupied the north in response to an Athens-engineered Greek Cypriot coup aimed at uniting the island with Greece.
The EU is pressing for a settlement by May 2004 when it is set to admit the internationally-recognized Greek Cypriot side. It says the Turkish Cypriots will be denied entry if a settlement is not struck in time.
Such a prospect threatens to spark tensions between the European Union and EU candidate Turkey, which maintains 30,000 soldiers in northern Cyprus.
Once the island joins the EU, Turkey could be considered an occupier of EU soil.
Ankara has suggested Cyprus peace talks could resume next month on the basis of a reunification plan put forward by UN Secretary General Kofi Annan, which Turkish Cypriot leader Rauf Denktash rejected in March last year.
The Turkish government is expected to set out its proposals following a key meeting of the National Security Council, which brings together the country's civilian and military leadership on 23 January.
Prodi was also to meet parliament speaker Bulent Arinc and President Ahmet Necdet Sezer before travelling to Istanbul on Friday to address Bosphorus University and inaugurate an EU information centre.