Turkey does not recognize Greek Cyprus as a sovereign nation and opposed Greek Cypriot presidency before a solution.
Ahmet Davutoğlu spoke on Thursday during a joint news conference with EU foreign policy chief Catherine Ashton and Enlargement Commissioner Stefan Füle.
EU candidate Turkey served notice last year that it would break off relations with the EU presidency during Greek Cyprus's six-month term unless there was progress in reunification talks between the Turkish Cypriots, living in the North, and Greek Cypriots who govern Greek Cyprus.
"Our position on the presidency of the Greek Cypriots is clear. Today we have once more conveyed our position in the meeting," Davutoğlu said.
"The relations and contacts with EU will continue, but none of the ministries, institutions of Turkish Republic will be in contact with the EU presidency in any of the activities related to Greek Cypriot presidency."
Turkey began formal entry negotiations for the European Union in 2005, a year after Greek Cyprus was admitted.
Its bid for membership virtually has ground to a halt due to the intractable dispute over the divided island and opposition from core EU members Germany and France.
Turkey failed last year to open a single new chapter, or policy area, that candidate countries must complete to meet EU norms.
Out of 35 chapters, 17 are blocked either by Greek Cyprus or France, 13 have been opened, one has been closed, and another four have yet to be opened. Eight policy issues have been frozen by the bloc over Turkey's refusal to allow ships and planes from Greek Cyprus enter its ports and airspace.
Greek Cyprus was split by a Turkish intervention in 1974 after a brief Greek-inspired coup. Since then, Turkey has bankrolled the Turkish Cypriot enclave in the north and kept a military presence there.
The European Union wants Turkey to throw open its ports and airports to traffic from Greek Cyprus to unfreeze some of the blocked chapters, but Turkey insists the European Union should end its embargo of the north at the same time.
The Cyprus dispute is a source of tension between fellow NATO members Greece and Turkey, and stakes were raised by a row over rights to hydrocarbon riches in the eastern Mediterranean following a discovery by Greek Cypriots last year that has been contested by Turkey.
Turkey, however, is showing renewed interest in reviving its stalled bid to join the European Union, now that one of its key opponents - Nicolas Sarkozy- is no longer the president of France.
Turkey began its EU accession negotiations in 2005 but made little progress in its candidacy, thanks to its dispute with Greek Cyprus and opposition from Sarkozy to Turkey's membership. Sarkozy argued that the predominantly Muslim country is not a part of Europe and wanted Turkey to accept some kind of a special partnership with the EU instead of full membership - an offer Turkey rejected.
Now that Socialist Francois Hollande has replaced the conservative Sarkozy as France's president, Turkey hopes France will be more sympathetic to the candidacy of a country that has one of the world's fastest growing economies and is becoming a regional diplomatic player.
"Turkey will determinedly progress in its course toward the EU," Egemen Bağış, the Turkish minister in charge of EU affairs, said Thursday.
Ashton, meanwhile, thanked Turkey for sheltering nearly 27,000 Syrian refugees who fled violence in neighboring Syria where forces loyal to President Bashar Assad are waging a crackdown on an uprising.